Changes in version 1.4.5
Bug fixes
- Chse where sex chromosomes were made lower case removed to match
UCSC
Changes in version 1.4.4
New features
- Further mappings added
Bug fixes
- Duplication of non-bi-allelic and indels fixed
- Correct compute_nsize documentation
Changes in version 1.4.0
New features
- Added "query" column to find_sumstats output to keep track of search
parameters.
- import_sumstats:
- Check if formatted file (save_path) exists before downloading to
save time.
- Pass up force_new in additional to force_new_vcf.
- Updated Description tag in DESCRIPTION file to better reflect the
scope of MungeSumstats.
- Upgraded read_vcf to be more robust.
- Edited Deps/Suggests
- Elevate IRanges to Imports.
- Remove stringr (no longer used)
- Add new internal function is_tabix to check whether a file is
already tabix-indexed.
- read_sumstats: now takes samples as an arg. By default, only uses
first sample (if multiple are present in file).
- Remove INFO_filter= from ALS VCF examples in vignettes (no longer
necessary now that INFO parsing has been corrected).
Bug fixes
- AF (allele frequency) was accidentally being assigned as INFO column
in VCFs where the INFO rows started with "AF". This caused a large
number of SNPs to be incorrectly dropped during the check_info_score
step.
- If INFO score is not available, INFO column is now dropped entirely
(rather than assigning all 1s).
- Adjusted test-vcf_formatting to reflect this. This avoids
ambiguity about whether the INFO score is real or not.
- check_info_score:
- Added extra messages in various conditions where INFO is not
used for filtering, and don't add log_files$info_filter in these
instances.
- Added unit tests.
- check_empty_cols was accidentally dropping more columns than it
should have.
- Fix GHA pkgdown building:
- The newest version of git introduced bugs when building pkgdown
sites from within Docker containers (e.g. via my Linux GHA
workflow). Adjusting GHA to fix this.
- Fix write_sumstats when indexing VCF.
- Ensure read_sumstats can read in any VCF files (local/remote,
indexed/non-indexed).
- Fix test-vcf_formatting.R
- line 51: had wrong AF value in string
- line 109: encountering error? due to duplicate SNPs?
- Fix test-check_impute_se_beta
- lines 51/52: setkey on SNP (now automatically renamed from ID by
read_vcf).
- Fix test-read_sumstats:
- standardising of headers is now handled internally by
read_sumstats.
- Ensure CHR is a character vector when being read in.
- line 44: Ensure extra cols in vcf_ss are dropped.
- parse_logs: Add lines to parsing subfunctions to allow handling of
logs that don't contain certain info (thus avoid warnings when
creating the final data.table).
- 'Avoid the use of 'paste' in condition signals' fixed:
- check_pos_se
- check_signed_col
- Used to rely on gunzip to read bgz files, but apparently this
functionality is no longer supported (possibly due to changes to how
Rsamtools::bgzip does compression in Bioc 3.15. Switched to using
fread + readLines in:
- read_header
- read_sumstats
- read_header: wasn't reading in enough lines to get past the VCF
header. Increase to readLines(n=1000).
- read_vcf: Would sometimes induce duplicate rows. Now only unique
rows are used (after sample and columns filtering).
- Issue with mix of chr:bp:a1:a2 and chr:bp and rs id resolved
Changes in version 1.3.19
Bug fixes
- format_sumstats can now import remote files (other than OpenGWAS).
New features
- New sumstatsColHeaders entries:
- "PosGRCh37" --> "BP"
- "testedAllele" --> "A1"
Changes in version 1.3.18
New features
- Can now handle general remote sumstats not just IEU GWAS
- More column header mappings
Changes in version 1.3.17
New features
- Clean up of column header mapping file, including FREQUENCY given
priority over MAF and addition of new CHR mappings.
Changes in version 1.3.15
Bug fixes
- Handle cases for multi-trait GWAS when P columns exists separate to
the trait specific P value so that when renaming occurs there isn't
two P columns. Inputted P column will be renamed to 'P_input'
- Issue where 'check allele flip' wasn't running when the sumstats had
all SNP IDs missing and incorrect direction of A1/A2 and effect
columns has now been fixed.
Changes in version 1.3.14
New features
- liftover
- Now exported function.
- Added args for more user flexibility.
- Uses GenomeInfoDb::mapGenomeBuilds to standardise build names.
- Warns users when mapped builds do not match one of the
conversion options.
- Choice to output as data.table or GRanges.
- Added units tests for exported version.
- standardise_sumstats_column_headers_crossplatform
- Exported as standardise_header while keeping the original
function name as an internal function (they call the same code).
- Added unit tests for exported version.
- Added chunks to *Getting started` vignette
- liftover tutorial
- "Quick formatting" of headers and file formats.
Bug fixes
- check_pos_se: Remove extra message() call around string.
- check_signed_col: Remove extra message() call around string.
- write_sumstats
- Added extra round of sorting when tabix_index=TRUE because this
is required for tabix.
Changes in version 1.3.13
New Features
- Additional mappings for CHR
- Make A1, A2 upper-case
Bug fixes
- Bug fix for dealing with imputing SNP ID when there are indels
Changes in version 1.3.11
New Features
- MungeSumstats can now handle Indels better. It will:
- Not impute the RS ID of a SNP for an Indel
- Not remove the Indel based on the RS ID not being present in the
SNP ref dataset.
- Not remove the Indel if it has the same base-pair location as a
SNP in the sumstats.
- Can now handle vcfs with extensions .vcf.tsv, .vcf.tsv.gz and
.vcf.tsv.bgz
Bug fixes
- For non-bi-allelic SNP runs, no longer remove duplicated SNPs based
on their base-pair position or their RS ID.
Changes in version 1.3.9
New Features
- Exported functions. Added examples and unit tests:
- compute_nsize
- standardise_sumstats_column_headers_crossplatform
- formatted_example
- New arguments:
- standardise_sumstats_column_headers_crossplatform: Added arg
uppercase_unmapped to to allow users to specify whether they
want make the columns that could not be mapped to a standard
name uppercase (default=TRUE for backcompatibility). Added arg
return_list to specify whether to return a named list (default)
or just the data.table.
- formatted_example: Added args formatted to specify whether the
file should have its colnames standardised. Added args sorted to
specify whether the file should sort the data by coordinates.
Added arg return_list to specify whether to return a named list
(default) or just the data.table.
- Removed codecode.yml and _pkgdown.yml files (no longer necessary).
- Added Issues templates for Bugs and Feature requests.
- Added .datatable.aware=TRUE to .zzz as extra precaution.
- vcf2df: Documented arguments.
- Made v2 of hex sticker: inst/hex/hex.png
Bug fixes
- Regenerated the gh-pages branch after it accidentally got deleted.
- Remove temporary docs/ folder.
- Updated GitHub Actions.
- Updated Dockerfile so it doesn't run checks (this is now take care
of by the GHA workflow).
- Added Windows-specific folders to .Rbuildignore.
- Made to_GRanges.R and to_VRanges.R file names lowercase to be
congruent with function names.
Changes in version 1.3.7
Bug fixes
- Bug in checking for bad characters in RSID fixed
Changes in version 1.3.6
New Features
- Columns Beta and Standard Error can now be imputed. However note
that this imputation is an approximation so could have an effect on
downstream analysis. Use with caution.
Changes in version 1.3.5
Bug fixes
- Flipping of Odds Ratio corrected (1/OR rather than -1*OR)
Changes in version 1.3.4
Bug fixes
- Issue downloading chain file resolved
Changes in version 1.3.3
New Features
- More mappings added to default mapping file.
Changes in version 1.3.2
Bug fixes
- Previously rsids with characters added (e.g. rs1234567w) would cause
an error when checking for the rsid on the reference genome. This
has been fixed and the correct rsid will now be imputed from the
reference genome for these cases.
Changes in version 1.3.1
New Features
- import_sumstats: Create individual folders for each GWAS dataset,
with a respective logs subfolder to avoid overwriting log files when
processing multiple GWAS.
- parse_logs: New function to convert logs from one or more munged
GWAS into a data.table.
- list_sumstats: New function to recursively search for local summary
stats files previously munged with MungeSumstats.
- Added new dataset inst/extdata/MungeSumstats_log_msg.txt to test
logs files.
- Added unit tests for list_sumstats and parse_logs.
- Added new Docker vignette.
- Updated GHA workflows using r_workflows.
- Remove docs/ folder as the website will now be pushed to the
gh-pages branch automatically by new GHA workflow.
- Made documentation in README more clear and concise.
- Added checks for p-values >1 or <0 via args convert_large_p and
convert_neg_p, respectively. These are both handled by the new
internal function check_range_p_val, which also reports the number
of SNPs found meeting these criteria to the console/logs.
- check_small_p_val records which SNPs were imputed in a more robust
way, by recording which SNPs met the criteria before making the
changes (as opposed to inferred this info from which columns are 0
after making the changes). This function now only handles
non-negative p-values, so that rows with negative p-values can be
recorded/reported separately in the check_range_p_val step.
- check_small_p_val now reports the number of SNPs <= 5e-324 to
console/logs.
- Unit tests have been added for both check_range_p_val and
check_small_p_val.
- parse_logs can now extract information reported by check_range_p_val
and check_small_p_val.
- New internal function logs_example provides easy access to log file
stored in inst/extdata, and includes documentation on how it was
created.
- Both check_range_p_val and check_small_p_val now use #'
@inheritParams format_sumstats to improve consistency of
documentation.
Bug fixes
- Reduced vignette sizes.
- Removed usage of suppressWarnings where possible.
- Deleted old .Rproj file and hidden folder (contained large files).
- Configured .Rproj so it doesn't store large data files.
- Fix badger issues: https://github.com/GuangchuangYu/badger/issues/34
- Prevent test-index_tabix.R from running due to errors (for now).
Changes in version 1.3.0
New Features
- Version bump to align with Bioconductor release 3.14.
Changes in version 1.1.27
Bug fixes
- validate_parameters can now handle ref_genome=NULL
- .tsv.gz no longer assigned suffix .tsv.
- Made code width <80 characters.
- Changed to_GRanges/to_GRanges functions to all-lowercase functions
(for consistency with other functions).
- Set nThread=1 in data.table test functions.
New Features
- Added tests for get_genome_builds
- Added early check for making sure the directory save_path is in was
actually created (as opposed to finding out at the very end of the
pipeline).
- Tabix-indexing now available for tabular output data.
- read_header and read_sumstats now both work with .bgz files.
Changes in version 1.1.26
New Features
- Extra mappings for FRQ column, see data("sumstatsColHeaders") for
details
Changes in version 1.1.23
New Features
- format_sumstats(FRQ_filter) added so SNPs can now be filtered by
allele frequency
- Mapping file now has mappings for allele frequency (AF) to FRQ
- VCF files with AF in INFO column e.g. 'AF=...' now converted to AF
column
- format_sumstats(frq_is_maf) check added to infer if FRQ column
values are minor/effect allele frequencies or not. frq_is_maf allows
users to rename the FRQ column as MAJOR_ALLELE_FRQ if some values
appear to be major allele frequencies
Changes in version 1.1.19
New Features
- get_genome_builds() can now be called to quickly get the genome
build without running the whole reformatting.
- format_sumstats(compute_n) now has more methods to compute the
effective sample size with "ldsc", "sum", "giant" or "metal".
- format_sumstats(convert_ref_genome) now implemented which can
perform liftover to GRCh38 from GRCh37 and vice-versa enabling
better cohesion between different study's summary statistics.
Changes in version 1.1.11
Bug fixes
- check_no_rs_snp can now handle extra information after an RS ID. So
if you have rs1234:A:G that will be separated into two columns.
- check_two_step_col and check_four_step_col, the two checks for when
multiple columns are in one, have been updated so if not all SNPs
have multiple columns or some have more than the expected number,
this can now be handled.
- Extra mappings for the FRQ column have been added to the mapping
file
New Features
- check_multi_rs_snp can now handle all punctuation with/without
spaces. So if a row contains rs1234,rs5678 or rs1234, rs5678 or any
other punctuation character other than , these can be handled.
- format_sumstats(path) can now be passed a dataframe/datatable of the
summary statistics directly as well as a path to their saved
location.
- Input summary statistics with A0/A1 corresponding to ref/alt can now
be handled by the mappign file as well as A1/A2 corresponding to
ref/alt.
Changes in version 1.1.2
New Features
- import_sumstats reads GWAS sum stats directly from Open GWAS. Now
parallelised and reports how long each dataset took to import/format
in total.
- find_sumstats searches Open GWAS for datasets.
- compute_z computes Z-score from P.
- compute_n computes N for all SNPs from user defined smaple size.
- format_sumstats(ldsc_format=TRUE) ensures sum stats can be fed
directly into LDSC without any additional munging.
- read_sumstats, write_sumstas, and download_vcf functions now
exported.
- format_sumstats(sort_coordinates=TRUE) sorts results by their
genomic coordinates.
- format_sumstats(return_data=TRUE) returns data directly to user. Can
be returned in either data.table (default), GRanges or VRanges
format using format_sumstats(return_format="granges").
- format_sumstats(N_dropNA=TRUE) (default) drops rows where N is
missing.
- format_sumstats(snp_ids_are_rs_ids=TRUE) (default) Should the SNP
IDs inputted be inferred as RS IDs or some arbitrary ID.
- format_sumstats(write_vcf=TRUE) writes a tabix-indexed VCF file
instead of tabular format.
- format_sumstats(save_path=...) lets users decide where their results
are saved and what they're named.
- When the save_path indicates it's in tempdir(), message warns users
that these files will be deleted when R session ends.
- Summary of data is given at the beginning and the end of
format_sumstats via report_summary().
- Readability of preview_sumstats() messages improved.
- New checks standard error (SE) must >0 and BETA (and other effect
columns) must not equal 0:
format_sumstats(pos_se=TRUE,effect_columns_nonzero=TRUE)
- Log directory containing all removed SNPs is now available and can
be changed to a different directory by setting:
format_sumstats(log_folder_ind=TRUE,log_folder=tempdir())
- All imputed data can now be identified with a column in the output
using: format_sumstats(imputation_ind=TRUE)
- Users can now input their own mapping file to be used for the column
header mapping in place of data(sumstatsColHeaders). See
format_sumstats(mapping_file = mapping_file).
Bug fixes
- CHR column now standardised (X and Y caps, no "chr" prefix).
- Allele flipping done on a per-SNP basis (instead of whole-column).
- Allele flipping now includes FRQ column as well as effect columns.
- The effect allele is now interpreted as the A2 allele consistent
with IEU GWAS VCF approach. A1 will always be the reference allele.
- read_vcf upgraded to account for more VCF formats.
- check_n_num now accounts for situations where N is a character
vector and converts to numeric.
Changes in version 1.1.1
Bug fixes
- Preprint publication citation added.
Changes in version 1.0.0
New Features
- MungeSumstats released to Bioconductor.