- Bug fix for check 3 in infer effect column - previously A1 & A2 were swapped when there were more matches for the ref genome in A1 rather than A2 which was incorrect. Corrected now so it will only be flipped when A2 has more matches to the reference genome.
- Handling of -log10 p-values (outside of VCFs) added.
- Mapping for OA (other Alllele) added to A1.
- Can now pass local chain files for liftover (
local_chain
informat_sumstats()
andliftover()
).
- Can now control what columns are checked for missing data (
drop_na_cols
informat_sumstats()
). By default, SNP, effect columns and P/N columns are checked. Set to Null to check all columns or choose specific columns.
- Force no tab indexing when writing removed rows of SNPs. This avoids any issues where missing data causes sort errors.
- Issue fixed when sorting CHR column based on a format when CHR column is a factor.
- Catch for overflow when NA's in SNP col for
check_no_rs_snp()
check withimputation_ind=TRUE
.
- Minor fix to
get_genome_builds()
to help with RAM & CPU usage during unit tests. No change in functionality for end user.
- For LDSC format, rename A1 and A2 as LDSC expects A1 to be the effect column rather than A2 (the opposite to MSS's default) - see more here. Although, this didn't seem to make any difference to results in tests, see more here.
- Remove unused argument
make_ordered
fromsort_coords()
- Issue fixed with check ldsc format wehn compute_n type chosen
- Speed up unit test timing for bioc checks (predominately for linux tests)
infer_eff_direction
parameter added so user can decide whether to run the check
- Typo in unit test for infer effect direction.
- IEU GWAS unit tests updated to account for server outages.
- Fixed column header mappings
- Made all uncorrected header names uppercase and removed duplicates
- "TOTALSAMPLESIZE" now maps to "N" instead of "NSTUDY"
- "MAJORALLELE", "MAJOR_ALLELE", "MAJOR-ALLELE", and "MAJOR ALLELE" now map to "A1" instead of "A2"
- Removed the mappings for "OR-A1", "OR.A1", "OR_A1", and "BETA1" because MSS assumes that A2 is the effect allele
- Removed mappings for "A1FREQ", "A1FRQ", "AF1", "FREQ.A1.1000G.EUR", "FREQ.A1.ESP.EUR", "FREQ.ALLELE1.HAPMAPCEU", "FREQ1", "FREQ1.HAPMAP", and "FRQ_A1" because MSS defines "FRQ" to be the allele frequency of A2
- Removed mappings for "CHR36", "BASE_GRCH36", "POSITION36", "POSGRCH36", "BASEGRCH36", "POS36", "POS GRCH36", "POS.GRCH36", "POS-GRCH36", and "POS_GRCH36" because MSS does not support the GRCh36 genome build
- Removed the ambiguous mapping "NMISS" -> "N" because "NMISS" can refer to the number of samples with missing data
- Removed the ambiguous mapping "WEIGHT" -> "N" because "WEIGHT" can refer to coefficient weights
- Fixed inference of allele where ambiguous (A1, A2) naming used (see
infer_effect_column.R for code) but in short:
- Three checks now made to infer which allele the effect/frequency information relates to. See infer_effect_column.R for further details.
- See get_eff_frq_allele_combns.R for how effect/frequency columns that infer the allele are captured in the mapping file
- New column header mappings:
- "VARIANT_ID" and "RSIDS" --> "SNP"
- "P_BOLT_LMM" --> "P"
- "NCASES" --> "N_CAS"
- "N_EFFECTIVE", "N_INFORMATIVE", and "TOTAL_N" --> "N"
- "HET_P" --> "HETPVAL"
- "HET_ISQ" --> "HETISQT"
- "ALL_AF" --> "FRQ"
- "DIRECT" --> "DIRECTION"
- "ALT_EFFSIZE" --> "BETA"
- "INFORMATIVE_ALT_AC" --> "AC"
- Cases checking ref genome where there are no indels would sometimes cause an error when joining. This resolved this issue.
- flip_frq_as_biallelic parameter added enabling frequencies of non-bi-allelic SNPs to be flipped as if they were bi-allelic (1 - frequency) i.e. ignoring the frequencies of other alternative alleles (assuming these will be negligible). Note this will not be done as default as it is not fully correct but may be useful for some users.
- Fix for imputation column when imputing RS ID from CHR:BP. Avoids crash and ensures correct identification of imputed SNPs.
- Avoid running compute_nsize function when no imputation is wanted by user - also avoids message output in this situation.
- Fix reporting of genome-wide sign variants before formatting.
- In
check_bp_range
ensure that the BP column is numeric.
- In
check_no_rs_snp
the order of operations had to be reversed to ensure all values were present before sorting column headers whenimputation_ind=TRUE
and imputing rsIDs.
- The
rmv_chrPrefix
parameter informat_sumstats()
has been replaced with the newchr_style
parameter, which allows users to specify their desired chromosome name style. The supported chromosome styles are "NCBI", "UCSC", "dbSNP", and "Ensembl" with "Ensembl" being the default. check_chr()
now automatically removes all SNPs with nonstandard CHR entries (anything other than 1-22, X, Y, and MT in the Ensembl naming style).
- Better method to detect vcf files - looks for vcf in extension not in name.
- Check ref genome change - if not match found for either genome build, an error will now be thrown.
- Checks has been added so that if chrom col has chr as a prefix, this will be removed before testing genome build.
- Bug fix when using imputation_ind with NA in chr column.
ignore_multi_trait
parameter added which will ignore any multi-trait p-values if set to TRUE. By default it is false to maintain the current default running conditions for MSS.
- Check added, ensure BP is between 1 - length of chromosome using reference chromosome.
- extra mapping for base-pair position (BP) column added
- Fix ensembl chain file retrieval so works on all environments
write_sumstats
:- Fix indexing issues due to incomplete genome coordinates sorting: https://github.com/neurogenomics/MungeSumstats/issues/117
- Add default
NULL
toref_genome
. - Check
ref_genome
(only in conditions where its used).
sort_coord
:- Renamed .R file from sort_coordinates to match current function name.
- Add multiple
sort_methods
, including improved/more robustdata.table
-native method. - Added dedicated unit tests within
test-index_tabular.R
.
- New helper function:
check_numeric
:- Ensures relevant sumstats cols are numeric.
- Added internally to:
sort_coord
,read_header
- rworkflows.yml:
- Omit Windows runner.
- Turn on
run_biocheck
- to_GRanges.R / to_VRanges.R:
- Rename files to match current function names.
- Remove extra extdata files (I think these were created by accident):
- ALSvcf.vcf.bgz
- ALSvcf.vcf.bgz.bgz
- ALSvcf.vcf.bgz.bgz.tbi
- ALSvcf.vcf.bgz.tbi
- ALSvcf.vcf.gz
- Remove .DS_Store files throughout.
- Don't check for duplicates based on RS ID with Indels, remove these first.
- Implement
rworkflows
.- Removed old Dockerfile (not needed anymore) and workflow yaml.
- Add
drop_indels
parameter so a user can decide to remove indels from sumstats.
- For downloading files use
sed -E
rather thansed -r
as its compatible with mac which has issues withsed -r
- For instances where a single column contains CHR, BP, A1 and A2. The default
order has been updated to CHR:BP:A1:A2 to align with
SPDI format. If your format differs and MSS doesn't pick up on it, update the column name to the true format e.g. CHR:BP:A2:A1
- Update to where SNP column is given by the four CHR, BP, A1, A2. Now, if A1 or A2 is also a separate column, these will be used to infer the order.
- further fix for Latex issues when rendering PDF of examples.
- fix for Latex issues when rendering PDF of examples.
- fix for offline runs and accessing chain files from 1.7.2.
- New chain files used for lifting over the genome build from Ensembl have now been added. These will now be set as the default chain file instead of UCSC due to licensing issues. The choice to use UCSC files will still be there but the files will not be stored in the package themselves, they will instead be downloaded for use on the fly.
- The use of the
log_folder
parameter informat_sumstats()
has been updated. It is still used to point to the directory for the log files and the log of MungeSumstats messages to be stored. And the default is still a temporary directory. However, now the name of the log files (log messages and log outputs) are the same as the name of the file specified in thesave_path
parameter with the extension '_log_msg.txt' and '_log_output.txt' respectively.
- GHA fix.
- By default ES taken as BETA new parameter added so users can specify if this
isn't the case (
es_is_beta
). If set to FALSE, mapping removed. - Imputing BETA ordering has been changed so log(OR) will be sued before calculating from Z, SE.
- A new method for computing the Z-score of a sumstats (
compute_z
input) has been added: BETA/SE. To use it setcompute_z = 'BETA'
to continue to use the P-value calculation usecompute_z = 'P'
. Note the default is stilcompute_z = FALSE
.
- Remove erroneous print statement.
- Fix NA representation for tabular outputs - By default,
data.table::fread()
leaves NAs blank instead of including a literal NA. That's fine for CSVs and if the output is read in by fread, but it breaks other tools for TSVs and is hard to read. Updated that and added a message when the table is switched to uncompressed for indexing.
read_header
:- Can now read entire files by setting
n=NULL
. - Improved reading in of VCF files (can read .vcf.bgz now).
- Now exported.
- Added unit tests.
- Can now read entire files by setting
- Remove
seqminer
from all code (too buggy). - Automatically remove residual .tsv files after tabix indexing.
import_sumstats
:- Use
@inheritDotParams format_sumstats
for better documentation.
- Use
parse_logs
: Added new fields.format_sumstats
: Added time report at the end (minutes taken total). Since this is a message, will be included in the logs, and is now parsed byparse_logs
and put into the column "time".
index_tabular
: Fixed by replacingseqminer
withRsamtools
.- When SNP ID's passed with format
1:123456789
, it will now be dealt with appropriately. compute_n
can't handle SNP level N values for imputation only population level. An explanatory error message has now been added.
- Special characters causing issues with find empty columns function. Now fixed.
- Mitchondrial (MT) SNPs' chromosome value were being forced to NA by sort_coords function. This has been fixed.
- Had to pass check_dups to other checks so they also wouldn't be run. Now independent of non-biallelic check.
- check_dups parameter added so duplicates won't be removed if formatting QTL datasets
- validate_parameters checks for incorrect version of dbSNP package, corrected.
- MSS can now impute CHR, BP at a SNP level. For cases where CHR and/or BP are NA but the RS ID is present, these will now be imputed fromt he reference genome. Note previously, this imputation was done when the chr and/or bp column was missing.
- Print statement from liftover silenced when no liftover required
- check missing data function will no longer remove cases with NA's in SNP_INFO column. The SNP_INFO column is created by MSS for cases with RS ID and some other information in the same SNP column (like rs1234:.....). Rather than throw out this info, it is stored in a new column - SNP_INFO. However, the remove missing data function was also looking in this column to remove SNPs. This has been corrected.
find_sumstats()
:- Fix N column in metadata.
- save_format parameter created for format_sumstats. This will replace ldsc_format which is now deprecated. Use save_format="LDSC" instead. Other options for save_format are generic standardised (NULL) and IEU Open GWAS VCF format ("openGWAS").
- dbSNP version 155 has now been added. Users can now control the version of dbSNP to be used for imputation (144 or 155). Note that with the 9x more SNPs in dbSNP 155 vs 144, run times will increase.
- Change where sex chromosomes were made lower case removed to match UCSC
- Further mappings added
- Duplication of non-bi-allelic and indels fixed
- Correct compute_nsize documentation
- Export
vcf2df
.- Move some post-processing function inside this function (e.g. drop duplicate cols/rows).
read_vcf
can now be parallised: splits query into chunks, imports them, and (optionally) converts them todata.table
before rbinding them back into one object.- Added report of VCF size (variants x samples) before processing to give user an idea of long it will take to process.
- Added arg
mt_thresh
to avoid using parallelisation when VCFs are small, due to the overhead outweighing the benefits in these cases.
- Added Linux installation instructions for axel downloader.
- Added 2nd
tryCatch
todownloader
with differentdownload.file
parameters that may work better on certain machines. - Avoid using
file.path
to specify URL in:get_chain_file
import_sumstats
- Allow
download_vcf
to pass URLs directly (without downloading the files) whenvcf_download=FALSE
. download_vcf
:- Make timeout 10min instead of 30min.
- Make axel verbose.
load_ref_genome_data
:- Give more informative messages that let user know which steps take a long time.
- Speed up substring preprocessing.
read_vcf_genome
: more robust way to get genome build from VCF.read_sumstats
: Speed up by usingremove_empty_cols(sampled_rows=)
, and only run for tabular file (read_vcf
already does this internally).
select_vcf_field
: Got rid of "REF col doesn't exists" warning by omittingrowRanges
.- Ensured several unevaluated code chunks in
vignettes/MungeSumstats.Rmd
were surrounding by ticks. vcf2df
: Accounted for scenarios wherewriteVcf
accidentally convertsgeno
data into redundant 3D matrices.- Use
data.table::rbindlist(fill=TRUE)
to bind chunks back together.
- Use
- Remove unused functions after
read_vcf
upgrades:infer_vcf_sample_ids
is_vcf_parsed
check_tab_delimited
read_vcf_data
remove_nonstandard_vcf_cols
- Remove redundant
dt_to_granges
by merging functionality intoto_granges
.- Adjusted
liftover
to accommodate the slight change.
- Adjusted
- Fix
is_tabix
(I had incorrectly madepath
all lowercase). - Let
index_vcf
recognize all compressed vcf suffixes.- Add extra error handling when .gz is not actually bgz-compressed.
- Set
BiocParallel
registered threads back to 1 afterread_vcf_parallel
finishes, to avoid potential conflicts with downstream steps.
- 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 toforce_new_vcf
.
- Check if formatted file (
- 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)
- Elevate
- Add new internal function
is_tabix
to check whether a file is already tabix-indexed. read_sumstats
:- now takes
samples
as an arg. - Parallises reading VCF using
GenomicFiles
.
- now takes
read_sumstats
: now takessamples
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). download_vcf
can now handle situations withvcf_url=
is actually a local file (not remote).
- 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.
- Added extra messages in various conditions where INFO is not
used for filtering,
and don't add
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 byread_vcf
).
- lines 51/52:
- 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.
- standardising of headers is now handled internally by
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 usingfread + readLines
in:read_header
read_sumstats
read_header
: wasn't reading in enough lines to get past the VCF header. Increase toreadLines(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
format_sumstats
can now import remote files (other than OpenGWAS).
- New
sumstatsColHeaders
entries:- "PosGRCh37" --> "BP"
- "testedAllele" --> "A1"
- Can now handle general remote sumstats not just IEU GWAS
- More column header mappings
- Clean up of column header mapping file, including FREQUENCY given priority over MAF and addition of new CHR mappings.
- 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.
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.
- Exported as
- Added chunks to *Getting started` vignette
liftover
tutorial- "Quick formatting" of headers and file formats.
check_pos_se
: Remove extramessage()
call around string.check_signed_col
: Remove extramessage()
call around string.write_sumstats
- Added extra round of sorting when
tabix_index=TRUE
because this is required for tabix.
- Added extra round of sorting when
- Additional mappings for CHR
- Make A1, A2 upper-case
- Bug fix for dealing with imputing SNP ID when there are indels
- 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
- For non-bi-allelic SNP runs, no longer remove duplicated SNPs based on their base-pair position or their RS ID.
- Exported functions. Added examples and unit tests:
compute_nsize
standardise_sumstats_column_headers_crossplatform
formatted_example
- New arguments:
standardise_sumstats_column_headers_crossplatform
: Added arguppercase_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 argreturn_list
to specify whether to return a named list (default) or just thedata.table
.formatted_example
: Added argsformatted
to specify whether the file should have its colnames standardised. Added argssorted
to specify whether the file should sort the data by coordinates. Added argreturn_list
to specify whether to return a named list (default) or just thedata.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
- 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.
- Bug in checking for bad characters in RSID fixed
- 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.
- Flipping of Odds Ratio corrected (1/OR rather than -1*OR)
- Issue downloading chain file resolved
- More mappings added to default mapping file.
- 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.
import_sumstats
: Create individual folders for each GWAS dataset, with a respectivelogs
subfolder to avoid overwriting log files when processing multiple GWAS.parse_logs
: New function to convert logs from one or more munged GWAS into adata.table
.list_sumstats
: New function to recursively search for local summary stats files previously munged withMungeSumstats
.- Added new dataset
inst/extdata/MungeSumstats_log_msg.txt
to test logs files. - Added unit tests for
list_sumstats
andparse_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
andconvert_neg_p
, respectively. These are both handled by the new internal functioncheck_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 thecheck_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
andcheck_small_p_val
. parse_logs
can now extract information reported bycheck_range_p_val
andcheck_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
andcheck_small_p_val
now use#' @inheritParams format_sumstats
to improve consistency of documentation.
- 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: GuangchuangYu/badger#34
- Prevent test-index_tabix.R from running due to errors (for now).
- Version bump to align with Bioconductor release 3.14.
validate_parameters
can now handleref_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
indata.table
test functions.
- 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
andread_sumstats
now both work with .bgz files.
- Extra mappings for FRQ column, see
data("sumstatsColHeaders")
for details
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
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.
check_no_rs_snp
can now handle extra information after an RS ID. So if you havers1234:A:G
that will be separated into two columns.check_two_step_col
andcheck_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
check_multi_rs_snp
can now handle all punctuation with/without spaces. So if a row containsrs1234,rs5678
orrs1234, 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 asA1/A2
corresponding to ref/alt.
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
, anddownload_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 eitherdata.table
(default),GRanges
orVRanges
format usingformat_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 intempdir()
, 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
viareport_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)
. Seeformat_sumstats(mapping_file = mapping_file)
.
- 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.
- Preprint publication citation added.
- MungeSumstats released to Bioconductor.