Changes in version 1.35.2
o Replace read.table and write.table with much faster
data.table::fread and data.table::fwrite in functions that
convert to and from text. The exception is
createAffyIntensityFile and
checkIntensityFile(affy.inten=TRUE), which still use read.table
to preserve the behavior of removing lines commented with the
"#" character.
Changes in version 1.27.1
o Add GenotypeIterator and GenotypeBlockIterator classes. These
classes allow returning blocks of SNPs with each call to
iterateFilter.
Changes in version 1.23.2
o Add a function to coerce a GenotypeData object to a VCF object
for use with VariantAnnotation.
Changes in version 1.23.1
o Move ncdf4 from Imports to Suggests. Users who wish to use
NetCDF files instead of GDS will have to install the ncdf4
package separately. This change eliminates the requirement to
install the NetCDF library on Linux machines for users who plan
to use GDS only.
Changes in version 1.21.1
o Replace ZIP_RA with LZMA_RA for GDS compression.
o Default is no compression for genotypes.
Changes in version 1.19.1
o Speed up corr.by.snp in duplicateDiscordance.
Changes in version 1.17.9
o Replace ncdf with ncdf4
o Deprecate plinkToNcdf and convertVcfGds (use SNPRelate
functions instead)
o Add function kingIBS0FSCI to define expected IBS0 spread of
full siblings based on allele frequency.
Changes in version 1.17.8
o do not compute qbeta for all points in qqPlot if thinning
Changes in version 1.17.7
o add error handling to close GdsGenotypeReader and
GdsIntensityReader gds files if they fail the validity method
check
Changes in version 1.17.6
o Use ZIP_RA as default compression in GDS files for faster
access to compressed data
Changes in version 1.17.5
o bug fix in checkImputedDosageFile if not writing a log file of
missing values and an entire sample is missing from the file
Changes in version 1.17.4
o bug fix for coloring truncated points in manhattanPlot
Changes in version 1.17.3
o added support for hard-calling genotypes from imputed genotype
probabilities in imputedDosageFile
Changes in version 1.17.1
o changed colors for ibdPlot
Changes in version 1.15.16
o added permute argument to exactHWE
Changes in version 1.15.15
o allow multiple color schemes for plots color-coded by genotype
Changes in version 1.15.13
o pedigreePairwiseRelatedness identifies great grandparent/great
grandchild (GGp) and grand avuncular (GAv)
Changes in version 1.15.12
o allow character scanID in createDataFile
Changes in version 1.15.11
o added col argument to manhattanPlot
Changes in version 1.15.10
o createDataFile converts non-finite values to NA.
Changes in version 1.15.8
o alleleFrequency includes scans with missing sex.
Changes in version 1.15.7
o Added option to reorder samples in vcfWrite.
Changes in version 1.15.5
o Added option to read genotypes coded with nucleotides in
createDataFile.
Changes in version 1.15.3
o Added beta and standard error for GxE term to assocRegression
output.
Changes in version 1.15.2
o Added number of cases and controls to assocRegression output.
Changes in version 1.15.1
o Added "ci" argument to qqPlot function.
Changes in version 1.13.27
o Added "snpID" and "scanID" arguments to getGenotypeSelection.
Changes in version 1.13.26
o Added getScanAnnotation, getSnpAnnotation accessors for
GenotypeData objects.
Changes in version 1.13.24
o Added data tables for genome build 38: centromeres.hg38.RData,
pseudoautosomal.hg38.RData, HLA.hg38.RData,
pcaSnpFilters.hg38.RData.
Changes in version 1.13.23
o convertGdsNcdf works for transposed (sample x snp) genotype
files.
Changes in version 1.13.22
o Removed "outfile" arguments from batchChisqTest,
batchFisherTest, and mendelErr. Saving output to a file should
happen outside the function calls.
o batchChisqTest and batchFisherTest have snp.include arguments
to run on individual SNPs. Using batchFisherTest with this
argument is recommended to replace the deprecated
assocTestFisherExact.
Changes in version 1.13.21
o assocRegression replaces assocTestRegression. Only one model is
allowed per function call.
o assocCoxPH replaces assocTestCPH. Output format is now similar
to assocRegression.
o exactHWE replaces gwasExactHWE.
o assocRegression, assocCoxPH, and exactHWE include the option to
select blocks of SNPs by index for easier parallelization.
o scan.chromosome.filter is no longer an option; use
setMissingGenotypes to filter data prior to running other
functions.
Changes in version 1.13.9
o Add use.names argument to getGenotype and getGenotype selection
o Add order=c("file", "selection") argument to
getGenotypeSelection
o duplicateDiscordanceAcrossDatasets and
dupDosageCorAcrossDatasets will not match on unmapped SNPs
Changes in version 1.13.8
o Add drop=TRUE argument to getVariable, etc.
Changes in version 1.13.7
o Add dupDosageCorAcrossDatasets.
o Add getGenotypeSelection method to MatrixGenotypeReader.
Changes in version 1.13.6
o Add getGenotypeSelection to select non-continguous SNPs and
scans from GDS files.
Changes in version 1.13.3
o Bug fix in imputedDosageFile - for IMPUTE2, include columns
from .samples file in output scan annotation.
Changes in version 1.11.33
o Allow getting variables from sub-nodes in a GDS file (e.g.,
getVariable(GdsReader, "snp.annot/qual")).
o Add getNodeDescription method to GdsReader.
o Added examples of converting from PLINK and VCF in Formats
vignette.
Changes in version 1.11.32
o imputedDosageFile replaces ncdfImputedDosage and
gdsImputedDosage
Changes in version 1.11.31
o setMissingGenotypes replaces ncdfSetMissingGenotypes and
gdsSetMissingGenotypes
Changes in version 1.11.22
o convertNcdfGds and convertGdsNcdf will convert files with any
variable names (not just genotype)
Changes in version 1.11.21
o Fixed bug in vcfWrite to output missing data code for ID column
o Data cleaning vignette uses createDataFile instead of
ncdfCreate and ncdfAddData
o Data cleaning vignette uses snpgdsOpen and snpgdsClose
Changes in version 1.11.20
o Fixed bug in assocTestCPH when there is no Y chromosome in the
data
Changes in version 1.11.19
o convertNcdfGds will not write entire snp and sample annotations
to file
o createDataFile replaces ncdfCreate and ncdfAddData
Changes in version 1.11.18
o patch from Karl Forner to allow use of open gds objects in
constructors for GdsReader and GdsGenotypeReader
Changes in version 1.11.17
o removed duplicated .probToDosage function from
ncdfImputedDosage.R source file
Changes in version 1.11.16
o expanded matching options in duplicateDiscordanceAcrossDatasets
Changes in version 1.11.15
o allowed truncate to be a numeric value or TRUE in qqPlot
Changes in version 1.11.14
o added pasteSorted function
Changes in version 1.11.13
o in case of missing allele code, return character genotype as NA
Changes in version 1.11.12
o bug fix in assocTestRegression when a block contains only 1 SNP
Changes in version 1.11.11
o added vcfCheck function to compare VCF file to GenotypeData
object
Changes in version 1.11.10
o bug fix in gwasExactHW when a block contains only 1 genotype
Changes in version 1.11.9
o changed colors of BAF plots so points can be more easily
distinguished
Changes in version 1.11.8
o added ref.allele option to vcfWrite to select either A or B as
the reference allele for each SNP
Changes in version 1.11.7
o added vcfWrite function to write VCF file from GenotypeData
object
Changes in version 1.11.6
o bug fix in qqPlot, manhattanPlot when requesting thinning when
bins only have 1 point
Changes in version 1.11.5
o added pointsPerBin argument to manhattanPlot
Changes in version 1.11.4
o added optional thinThreshold argument to manhattanPlot and
qqPlot functions
Changes in version 1.11.3
o updated gdsSubset for new gdsfmt read.gdsn syntax (also changed
in release version)
Changes in version 1.11.1
o Added ylim argument to qqPlot.
Changes in version 1.9.9
o added block size support for GDS files stored with scan,snp
dimensions
o gdsSubset and gdsSubsetCheck now operate on the fastest
dimension of the GDS file
Changes in version 1.9.8
o updates/bug fixes to gdsSubset/gdsSubsetCheck - different
missing value attributes may be set if sub.storage type is
different.
Changes in version 1.9.7
o Added gdsSubset and gdsSubsetCheck functions to make a subset
GDS file that includes only specified SNPs and scans from an
existing GDS file
o Updated gdsImputedDosage and gdsCheckImputedDosage to account
for IMPUTE2 gprobs files that have missing values (specified by
three equal probability strings)
o Updated gdsCheckImputedDosage to produce optional logfile
reporting any missing genotypes
Changes in version 1.9.6
o Revised anomFilterBAF - fewer centromere spanning anomalies
that aren't real, corrects some merging issues (previously it
would merge sections that really were different split widths).
Users should be aware that this will increase running time.
Changes in version 1.9.5
o Remove defunct functions.
o Improve efficiency of gwasExactHW, mendelErr,
assocTestRegression (reduce number of calls to rbind).
Changes in version 1.9.4
o Bug fix in getChromosome method for SnpAnnotationDataFrame
(proper behavior of unnamed "index" argument).
Changes in version 1.9.3
o Added gdsImputedDosage function.
o GdsGenotypeReader can return transposed genotypes.
Changes in version 1.9.2
o ScanAnnotationDataFrame and ScanAnnotationSQLite allow
non-integer scanID.
o Fix getAlleleA and getAlleleB in GdsGenotypeReader to work with
indels.
Changes in version 1.9.1
o Documentation now located in vignettes/ folder.
o Added ibdAssignRelationshipsKing.
o Added support for genotype GDS files with scan x snp dimensions
in GdsGenotypeReader.
Changes in version 1.7.8
o Added gdsSetMissingGenotypes, updated argument names in
ncdfSetMissingGenotypes.
o Changed colorscheme in manhattanPlot.R.
o Bug fix in ibdPlot - diagonal orange bars are back.
o Bug fix in plinkWrite for writing just one sample.
o Bug fix in printing pedigreeCheck error message.
Changes in version 1.7.7
o Changed handling of GxE interaction variables in
assocTestRegression.
Changes in version 1.7.6
o Updated vignette for SNPRelate 0.9.16.
Changes in version 1.7.5
o gwasExactHW will run on all chromosomes except (Y,M), rather
than (autosome,X,XY) only.
Changes in version 1.7.4
o More informative error messages in anomDetectBAF and
anomDetectLOH.
Changes in version 1.7.3
o Changed labeling of IBD plots from "HS" to "Deg2" and "FC" to
"Deg3."
o Bug fix in pedigreePairwiseRelatedness - no more warning about
multiple values passed to stringsAsFactor.
o pedigreeClean and pedigreeFindDuplicates are now defunct. Use
pedigreeCheck instead.
Changes in version 1.5.9
o assocTestRegression computes allele counts separately for each
model.
o convertNcdfGds uses information from a SnpAnnotationDataFrame
to store allele and chromosome codes in the GDS file.
Changes in version 1.5.8
o Adding missing value support to GdsReader.
o Fixed bug in getAttribute method for GdsReader.
o Updated GdsReader for compatibility with gdsfmt 0.9.11 (no
longer compatible with older versions).
Changes in version 1.5.7
o Fixed bug in genotypeToCharacter that resulted in calls to
getGenotype(char=TRUE) for a single SNP to return NA.
o Renamed minorAlleleSensitivitySpecificity to
minorAlleleDetectionAccuracy and added additional output.
Changes in version 1.5.6
o Added function minorAlleleSensitivitySpecificity.
Changes in version 1.5.5
o Deprecated pedigreeClean and pedigreeFindDuplicates.
pedigreeCheck now encompasses all pedigree checks and should be
used instead.
o Added pedigreeMaxUnrelated to find the maximum set of unrelated
members of a pedigree.
o Added additional output column "MAF" to matrix returned by
alleleFrequency.
Changes in version 1.5.4
o Removed hard-coding of autosomes as 1:22; can now set a vector
of integer codes corresponding to autosomes with "autosomeCode"
argument at object creation and retrieve with "autosomeCode"
methods. This change makes GWASTools compatible with non-human
organisms.
o Added option to duplicateDiscordanceAcrossDatasets to count
missing data as discordance.
o Added option to start axes of genoClusterPlot at 0.
Changes in version 1.5.3
o Removed "alleleA.col" and "alleleB.col" options from plink
functions, as "alleleA" and "alleleB" are now standard names.
o Added "getAlleleA" and "getAlleleB" methods to
GdsGenotypeReader.
o Added "getDimension" method to NcdfReader.
Changes in version 1.5.2
o Added "getAlleleA" and "getAlleleB" methods to SnpAnnotation*
and GenotypeData objects.
o Added genotypeToCharacter function to convert genotypes from
number of A alleles to A/B format.
o getGenotype for GenotypeData has option char=TRUE to return
character genotypes in A/B format.
Changes in version 1.5.1
o Added option to duplicateDiscordanceAcrossDatasets to calculate
minor allele discordance.
Changes in version 1.3.16
o Added convertVcfGds to extract bi-allelic SNPs from a VCF file.
o Added ncdfImputedDosage to convert output from common
imputation programs to NetCDF. assocTestRegression has an
additional argument dosage=TRUE to be used with these files.
o Added vignette describing GWASTools data structures.
Changes in version 1.3.15
o Bug fix in pedigreePairwiseRelatedness related to use of
character identifiers.
Changes in version 1.3.14
o assocTestRegression returns NA for snps where cases or controls
are monomorphic, added assocTestFisherExact to use in that
case.
o Added snp.exclude argument to pseudoautoIntensityPlot.
o Bug fix in messages reporting file read times when creating or
checking netCDF files.
Changes in version 1.3.13
o Added vignette on converting VCF to NetCDF with annotation.
o Prevent duplicateDiscordance from checking correlation by SNP
in cases of no variation.
Changes in version 1.3.12
o Added GdsReader and GdsGenotypeReader classes with dependency
on gdsfmt. GenotypeData objects can also be created with
GdsGenotypeReader objects in the "data" slot.
Changes in version 1.3.11
o Fixed bug in duplicateDiscordance when Y chromosome is not
included.
Changes in version 1.3.10
o Fixed bug in chromIntensityPlot so ideogram scales correctly if
SNPs are excluded.
Changes in version 1.3.9
o Fixed bug in assocTestCPH that could lead to false positives if
additive model failed but GxE model did not.
o Allow multiple variables for stratified analysis in
assocTestCPH.
Changes in version 1.3.8
o Pedigree functions accept non-numeric identifiers and provide
additional output.
Changes in version 1.3.7
o In batchChisqTest, Yates correction cannot be bigger than the
terms it corrects. Changed to match bug fix to chisq.test in R
2.15.1.
Changes in version 1.3.6
o Removed automatic subtitle from qqPlot.
o Allow selection of theoretical boundaries to draw in ibdPlot.
Changes in version 1.3.5
o Added function asSnpMatrix to convert a GenotypeData object to
a SnpMatrix object for use with snpStats.
Changes in version 1.3.4
o Added chromosome ideograms to chromIntensityPlot and
anomStatsPlot. anomStatsPlot has an option to put multiple
anomalies on the same plot.
Changes in version 1.3.3
o Updated vignette.
Changes in version 1.3.2
o Use lazy loading of data.
o manhattanPlot and snpCorrelationPlot accept character vectors
of chromosome; chrom.labels argument no longer used.
Changes in version 1.3.1
o close method of NcdfReader returns invisibly.
Changes in version 1.1.9
o anomSegStats checks for SNPs in centromere gaps.
o anomStatsPlot has option to plot LRR/BAF individually (for
greater flexibility in layout).
o Updates to arguments for plot titles in chromIntensityPlot,
anomStatsPlot, and pseudoautoIntensityPlot for consistency.
o plinkCheck has map.alt argument to override default
GenotypeData -> PLINK annotation conversion.
Changes in version 1.1.8
o Updated positions of pseudoautosomal regions.
o Added plinkToNcdf to convert PLINK files to NetCDF for use in
GWASTools.
Changes in version 1.1.7
o chromIntensityPlot and pseudoautoIntensityPlot have cex=0.5 by
default.
o chromIntensityPlot colors now match anomStatsPlot colors.
o plinkCheck has options to skip checking parents and sex.
o plinkCheck sorts alleles by character to avoid phase
mismatches.
o plinkWrite and plinkCheck print progress messages if
verbose=TRUE.
Changes in version 1.1.6
o duplicateDiscordance and duplicateDiscordanceAcrossDatasets use
only one pair of scans per subject by default.
o duplicateDiscordanceProbability sets small negative values to
0.
Changes in version 1.1.5
o duplicateDiscordance has an option to compute correlation by
SNP.
o Added scan.exclude argument to plinkCheck.
Changes in version 1.1.4
o Added ncdfSetMissingGenotypes function.
o plinkCheck now writes a log file with all mismatches found.
o duplicateDiscordance excludes Y chrom SNPs for females.
o duplicateDiscordance has an option to consider only pairs
involving the minor allele.
Changes in version 1.1.3
o batchChisqTest and batchFisherTest now return n results for n
batches even if n=2.
o batchFisherTest has return.by.snp=FALSE as default.
Changes in version 1.1.2
o Added LR tests to assocTestRegression.
o Bug fix in calculation of mean odds ratio in batchFisherTest.
o Bug fix in missingGenotypeByScanChrom for data sets with only
one female.
Changes in version 1.1.1
o Added functions plinkWrite and plinkCheck for writing and
checking PLINK ped and map files.
o Added pcaSnpFilters data set for identifying regions with high
PC-SNP correlation.