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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MungeSumstats.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MungeSumstats_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/MungeSumstats.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MungeSumstats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MungeSumstats' version '1.4.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'MungeSumstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
get_genome_builds 88.83   3.69  280.77
format_sumstats   49.58   2.22  162.61
read_vcf           4.62   0.32   14.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MungeSumstats
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MungeSumstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MungeSumstats)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MungeSumstats)
> 
> test_check("MungeSumstats")
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3a8e7922.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c185145aa
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A0	A1	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3a8e7922.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c729b7b9b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c185145aa
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c729b7b9b.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Sorting coordinates.
Filtering SNPs based on INFO score.
46 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/info_filter.tsv.gz
INFO_filter==0. Skipping INFO score filtering step.
Filtering SNPs based on INFO score.
All rows have INFO>=0.9
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Sorting coordinates.
3 p-values are >1 which LDSC/MAGMA may not be able to handle. These will be converted to 1.
5 p-values are <0 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Sorting coordinates.
8 p-values are <=5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
VCF format detected.This will be converted to a standardised table format.
Importing tabular file: F:/biocbuild/bbs-3.15-bioc/R/library/MungeSumstats/extdata/eduAttainOkbay.txt
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)`
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1a0028c5.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7331b87
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP_A2_A1 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file: 
SNP	FRQ	BETA	SE	P	CHR	BP	A2	A1	
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1a0028c5.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2b063a75.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7331b87
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2b063a75.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1f9146c.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7ca4535
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	EAF	Beta	SE	Pval	CHR_BP_A2_A1	CHR_BP_A2_A1_2	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position:A2:A1.
The column CHR_BP_A2_A1_2 will be kept whereas the column(s) CHR_BP_A2_A1 will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column CHR_BP_A2_A1_2 has been separated into the columns CHR, BP, A2, A1
Standardising column headers.
First line of summary statistics file: 
SNP	FRQ	BETA	SE	P	CHR	BP	A2	A1	
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1f9146c.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6dfe1713.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7ca4535
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6dfe1713.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5cce39d8.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c68b1129a
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	EAF	Beta	SE	Pval	alleles	allele	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Warning: Multiple columns in the sumstats file seem to relate to alleles A1>A2.
The column ALLELES will be kept whereas the column(s) ALLELE will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column ALLELES has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5cce39d8.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c48c64697.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c68b1129a
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c48c64697.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6a086e75.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c395b7706
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	CHR	BP	
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6a086e75.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c48332a5b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c395b7706
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c48332a5b.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c66eb1e82.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3efd6af8
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	A1	A2	EAF	Beta	SE	Pval	CHR_BP	CHR_BP_2	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position.
The column CHR_BP_2 will be kept whereas the column(s) CHR_BP will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before 
running `format_sumstats()`.
Column CHR_BP_2 has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
SNP	A1	A2	FRQ	BETA	SE	P	CHR	BP	
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c66eb1e82.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d673ebd.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3efd6af8
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d673ebd.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c83c424e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c62a12bf0
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c83c424e.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c156f1505.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c153e291e
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c156f1505.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Setting sorted=FALSE (required when formatted=FALSE).
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Assigning N=1000 for all SNPs.
N already exists within sumstats_dt.
[1] "Testing: compute_n='ldsc'"
Computing effective sample size using the LDSC method:
 Neff = (N_CAS+N_CON) * (N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))[(N_CAS+N_CON)==max(N_CAS+N_CON)]))
[1] "Testing: compute_n='giant'"
Computing effective sample size using the GIANT method:
 Neff = 2 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='metal'"
Computing effective sample size using the METAL method:
 Neff = 4 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='sum'"
Computing sample size using the sum method:
 N = N_CAS + N_CON
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c58837492.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1b362b7b
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c58837492.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c635f4864.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Saving output messages to:
F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/MungeSumstats_log_msg.txt
Any runtime errors will be saved to:
F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/MungeSumstats_log_output.txt
Messages will not be printed to terminal.
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c663885b.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c758347cc
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c663885b.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d1d161f.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c72ee4eed
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 186 rows
   - 93 unique variants
   - 140 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
93 sumstat rows are duplicated. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d1d161f.tsv.gz
Summary statistics report:
   - 93 rows (50% of original 186 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c4f2c450c.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c72ee4eed
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c4f2c450c.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7f848bb.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c72ee4eed
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 94 rows
   - 94 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
1 base-pair positions are duplicated in the sumstats file. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Checking for bi-allelic SNPs.
Loading reference genome data.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7f848bb.tsv.gz
Summary statistics report:
   - 93 rows (98.9% of original 94 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5005311c.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3a6c7868
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Filtering effect columns, ensuring none equal 0.
5 SNPs have effect values = 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5005311c.tsv.gz
Summary statistics report:
   - 88 rows (94.6% of original 93 rows)
   - 88 unique variants
   - 65 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c25cb737c.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c26fa39a9
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	FRQ	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c25cb737c.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P      FRQ
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1.863269
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1.169733
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3bd26aec.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c26fa39a9
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	FRQ	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=FALSE, the FRQ column will be renamed MAJOR_ALLELE_FRQ to differentiate the values from 
minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3bd26aec.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08
   MAJOR_ALLELE_FRQ
1:         1.863269
2:         1.169733
3:         1.401423
4:         1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c25723eb2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c67f82b76
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c25723eb2.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6a971ebc.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c770a66db
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	INFO	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
Filtering SNPs based on INFO score.
38 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/info_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
28 SNPs (50.9%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6a971ebc.tsv.gz
Summary statistics report:
   - 55 rows (59.1% of original 93 rows)
   - 55 unique variants
   - 41 genome-wide significant variants (P<5e-8)
   - 16 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P     INFO
1: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1.863269
2: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1.169733
3:  rs1008078   1 91189731  T  C 0.37310 -0.016 0.003 6.005e-10 1.401423
4: rs61787263   1 98618714  T  C 0.76120  0.016 0.003 5.391e-08 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3c3d3c0b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c468a140b
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3c3d3c0b.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6d1f4b80.tsv.gz
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6d1f4b80.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file1\\file1836c3156f87.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file2\\file1836c5d772925.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file3\\file1836c696932f0.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file4\\file1836c7c4136bb.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file5\\file1836c22642d.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file6\\file1836cc1e798c.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file7\\file1836c4a5c63e1.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file8\\file1836c43c390f.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file9\\file1836c2cd423d6.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.15-bioc\\tmpdir\\RtmpoXykTf/data/file10\\file1836c444658e5.tsv.gz"
10 file(s) found.
Parsing info from 10 log file(s).
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6fda6a5e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2b32558
Checking for empty columns.
Removing 1 empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
WARNING: 1 rows in sumstats file are missing data and will be removed.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
46 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6fda6a5e.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2    FRQ   BETA    SE         P
1: rs10061788   5 87934707  A  G 0.2164  0.021 0.004 2.464e-09
2:  rs1007883  16 51163406  T  C 0.3713 -0.015 0.003 5.326e-08
3:  rs1008078   1 91189731  T  C 0.3731 -0.016 0.003 6.005e-10
4:  rs1043209  14 23373986  A  G 0.6026  0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c463834e6.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2b32558
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c463834e6.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2    FRQ   BETA    SE         P
1: rs10061788   5 87934707  A  G 0.2164  0.021 0.004 2.464e-09
2:  rs1007883  16 51163406  T  C 0.3713 -0.015 0.003 5.326e-08
3:  rs1008078   1 91189731  T  C 0.3731 -0.016 0.003 6.005e-10
4:  rs1043209  14 23373986  A  G 0.6026  0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c83e2aef.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6eb535df
Checking for empty columns.
Removing 1 empty columns.
Standardising column headers.
First line of summary statistics file: 
chromosome	rs_id	markername	position_hg18	Effect_allele	Other_allele	EAF_HapMapCEU	N_SMK	Effect_SMK	StdErr_SMK	P_value_SMK	N_NONSMK	Effect_NonSMK	StdErr_NonSMK	P_value_NonSMK	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 1 chromosomes
Checking for multi-GWAS.
WARNING: Multiple traits found in sumstats file only one of which can be analysed: 
SMK, NONSMK
Standardising column headers.
First line of summary statistics file: 
CHR	SNP	MARKERNAME	POSITION_HG18	A2	A1	EAF_HAPMAPCEU	N	EFFECT	STDERR	P_VALUE	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK	
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
1 SNP IDs are not correctly formatted and will be removed.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column MARKERNAME has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file: 
CHR	SNP	POSITION_HG18	A2	A1	EAF_HAPMAPCEU	N	BETA	SE	P	N_NONSMK	EFFECT_NONSMK	STDERR_NONSMK	P_VALUE_NONSMK	BP	
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c83e2aef.tsv.gz
Summary statistics report:
   - 4 rows (80% of original 5 rows)
   - 4 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
         SNP  CHR        BP A1 A2 POSITION_HG18 EAF_HAPMAPCEU     N    BETA
1: rs1000050 chr1 161003087  C  T     161003087        0.9000 36257  0.0001
2: rs1000073 chr1 155522020  G  A     155522020        0.3136 36335  0.0046
3: rs1000075 chr1  94939420  C  T      94939420        0.3583 38959 -0.0013
4: rs1000085 chr1  66630503  G  C      66630503        0.1667 38761  0.0053
       SE      P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
1: 0.0109 0.9931   127514        0.0058        0.0059         0.3307
2: 0.0083 0.5812   126780        0.0038        0.0045         0.3979
3: 0.0082 0.8687   147567       -0.0043        0.0044         0.3259
4: 0.0095 0.5746   147259       -0.0034        0.0052         0.5157
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1219732d.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c49497bbd
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	N_fixed	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1219732d.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N N_FIXED
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 5       5
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 1       1
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 1       1
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 7       7
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c47b44cd2.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c249197
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c47b44cd2.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5a26a9e.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c249197
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/n_large.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5a26a9e.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2bffe8f.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c249197
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	N	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/n_large.tsv.gz
Removing rows where is.na(N)
0 SNPs have N values that are NA and will be removed.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/n_null.tsv.gz
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
N already exists within sumstats_dt.
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2bffe8f.tsv.gz
Summary statistics report:
   - 92 rows (98.9% of original 93 rows)
   - 92 unique variants
   - 69 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P N
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08 3
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10 5
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14 3
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5bf7d86.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c78bb1527
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 23 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
3 SNPs are on chromosomes X, Y, MT and will be removed
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf/chr_excl.tsv.gz
Warning: When method is an integer, must be >0.
45 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5bf7d86.tsv.gz
Summary statistics report:
   - 90 rows (96.8% of original 93 rows)
   - 90 unique variants
   - 67 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d924b2c.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c78bb1527
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2d924b2c.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6dfc39f0
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c4cf96b99
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
SNP	CHR	BP	A1	A2	FRQ	BETA	SE	P	
Sorting coordinates.
Writing in VCF format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6a4626b7.vcf.gz
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Compressing and tabix-indexing VCF file.
Finding empty VCF columns based on first 1e+07 rows.
Converting VCF to data.table.
Checking for empty columns.
Removing 1 empty columns.
Time difference of 0.3 secs
7 empty column(s) detected.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file.
Time difference of 1.3 secs
Converting VCF to data.table.
Checking for empty columns.
Removing 3 empty columns.
Time difference of 0.2 secs
Checking for empty columns.
No INFO (SI) column detected.
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
ID	chr	BP	end	REF	ALT	SNP	FRQ	BETA	SE	P	
Compressing and tabix-indexing VCF file.
Finding empty VCF columns based on first 1e+07 rows.
Converting VCF to data.table.
Checking for empty columns.
Removing 2 empty columns.
Time difference of 0.3 secs
6 empty column(s) detected.
1 sample detected: EBI-a-GCST005647
Constructing ScanVcfParam object.
Reading VCF file.
Time difference of 1.7 secs
Converting VCF to data.table.
Checking for empty columns.
Removing 2 empty columns.
Time difference of 0.2 secs
Dropping 2 duplicate columns.
Checking for empty columns.
Unlisting 4 columns.
Renaming ID as SNP.
VCF file has -log10 P-values, these will be  converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file: 
SNP	chr	BP	end	REF	ALT	FILTER	AF	ES	LP	SE	P	
Sorting coordinates.
Writing in VCF format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c350f714f.vcf.gz
Converting summary statistics to Genomic Ranges.
Converting summary statistics to VRanges.
Compressing and tabix-indexing VCF file.
Finding empty VCF columns based on first 1e+07 rows.
Converting VCF to data.table.
Checking for empty columns.
Removing 3 empty columns.
Time difference of 0.2 secs
6 empty column(s) detected.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file.
Time difference of 1.1 secs
Converting VCF to data.table.
Checking for empty columns.
Removing 3 empty columns.
Time difference of 0.1 secs
Checking for empty columns.
VCF file has -log10 P-values, these will be  converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file: 
ID	chr	BP	end	REF	ALT	SNP	END	FILTER	FRQ	BETA	LP	SE	P	
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c34e21989.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Standardising column headers.
First line of summary statistics file: 
SNP	P	FRQ	BETA	CHR	BP	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
5 SNP IDs contain other information in the same column. These will be separated.
Checking for merged allele column.
Column SNP_INFO has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c34e21989.tsv.gz
Summary statistics report:
   - 5 rows (100% of original 5 rows)
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR    BP A1 A2           P       FRQ      BETA
1: rs140052487   1 54353  C  A 0.037219838 0.3000548 0.8797957
2: rs558796213   1 54564  G  T 0.004382482 0.5848666 0.7068747
3: rs561234294   1 54591  A  G 0.070968402 0.3334671 0.7319726
4:   rs2462492   1 54676  C  T 0.065769040 0.6220120 0.9316344
Returning data directly.
******::NOTE::******
 - Log results will be saved to `tempdir()` by default.
 - This means all log data from the run will be  deleted upon ending the R session.
 - To keep it, change `log_folder` to an actual directory  (e.g. log_folder='./').
 ******************** 

Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c178d6fb3.tsv.gz
Log data to be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf
Standardising column headers.
First line of summary statistics file: 
SNP	P	FRQ	BETA	CHR	BP	A1	A2	
Summary statistics report:
   - 5 rows
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c178d6fb3.tsv.gz
Summary statistics report:
   - 5 rows (100% of original 5 rows)
   - 5 unique variants
   - 0 genome-wide significant variants (P<5e-8)
   - 1 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
           SNP CHR    BP A1 A2           P       FRQ      BETA
1: rs140052487   1 54353  C  A 0.037219838 0.3000548 0.8797957
2: rs558796213   1 54564  G  T 0.004382482 0.5848666 0.7068747
3: rs561234294   1 54591  A  G 0.070968402 0.3334671 0.7319726
4:   rs2462492   1 54676  C  T 0.065769040 0.6220120 0.9316344
Returning data directly.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3db26c79.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c56a9528a
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c557e4e3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c74ac3040
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c557e4e3.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c404a3981.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c74ac3040
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c404a3981.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c13286d29.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c5fd84ab3
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c13286d29.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c72053337.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c51d250d2
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c72053337.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1d3a5fc3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c36fe77a6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
5 SNPs have SE values <= 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted  summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A1FREQ, A1FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, AF1, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.A1.1000G.EUR, FREQ.A1.ESP.EUR, FREQ.ALLELE1.HAPMAPCEU, FREQ.B, FREQ1, FREQ1.HAPMAP, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_A1, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1d3a5fc3.tsv.gz
Summary statistics report:
   - 88 rows (94.6% of original 93 rows)
   - 88 unique variants
   - 65 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     FRQ   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	Support	
Returning unmapped column names without making them uppercase.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	Support	
Returning unmapped column names without making them uppercase.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c20fb2566.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c53d720b3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c2526393f
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Removing 'chr' prefix from CHR.
Making X/Y CHR uppercase.
Warning: When method is an integer, must be >0.
Could not recognize genome build of:
 - target_genome
These will be inferred from the data.
Sorting coordinates.
Writing in tabular format ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c53d720b3.tsv.gz
Summary statistics report:
   - 93 rows (100% of original 93 rows)
   - 93 unique variants
   - 70 genome-wide significant variants (P<5e-8)
   - 20 chromosomes
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR       BP A1 A2     EAF   BETA    SE         P
1:   rs301800   1  8490603  T  C 0.17910  0.019 0.003 1.794e-08
2: rs11210860   1 43982527  A  G 0.36940  0.017 0.003 2.359e-10
3: rs34305371   1 72733610  A  G 0.08769  0.035 0.005 3.762e-14
4:  rs2568955   1 72762169  T  C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Converting summary statistics to Genomic Ranges.
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1d9f23b1.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c105a1af0.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c59bc1bf8.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1a195205.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c71101e01.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c7d9241fe.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836cb0359ae.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c3c90f72.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c4fe33aec.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c1ae63d49.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c44345093.tsv.gz
Formatted summary statistics will be saved to ==>  F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c6e471a8e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpoXykTf\file1836c74606ac6
Checking for empty columns.
Standardising column headers.
First line of summary statistics file: 
MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	
Summary statistics report:
   - 93 rows
   - 93 unique variants
   - 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 129 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
  87.56    3.57   94.93