Package: MungeSumstats 1.21.0

Alan Murphy

MungeSumstats: Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Authors:Alan Murphy [aut, cre], Brian Schilder [aut, ctb], Nathan Skene [aut]

MungeSumstats_1.21.0.tar.gz
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MungeSumstats_1.21.0.tgz(r-4.6-any)MungeSumstats_1.21.0.tgz(r-4.5-any)
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MungeSumstats_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MungeSumstats/json (API)
NEWS

# Install 'MungeSumstats' in R:
install.packages('MungeSumstats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/neurogenomics/mungesumstats/issues

Pkgdown/docs site:https://al-murphy.github.io

Datasets:

On BioConductor:MungeSumstats-1.21.0(bioc 3.24)MungeSumstats-1.20.0(bioc 3.23)

snpwholegenomegeneticscomparativegenomicsgenomewideassociationgenomicvariationpreprocessing

6.53 score 3 stars 176 scripts 1.2k downloads 19 exports 85 dependencies

Last updated from:d3c05cb3f8. Checks:6 WARNING, 3 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING436
linux-devel-x86_64ERROR938
source / vignettesERROR529
linux-release-x86_64WARNING1104
macos-release-arm64WARNING1981
macos-oldrel-arm64WARNING2799
windows-develERROR734
windows-releaseWARNING803
windows-oldrelWARNING787
wasm-releaseOK338

Exports:compute_nsizedownload_vcffind_sumstatsformat_sumstatsformatted_exampleget_genome_buildsimport_sumstatsindex_tabularinfer_effect_columnliftoverlist_sumstatsload_snp_loc_dataparse_logsread_headerread_sumstatsread_vcfstandardise_headervcf2dfwrite_sumstats

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrieugwasrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngR.methodsS3R.ooR.utilsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Ensures that parameters are compatible with LDSC formatcheck_ldsc_format
Check for N column if not present and user wants, impute N based on user's sample size. *NOTE* this will be the same value for each SNP which is not necessarily correct and may cause issues down the line. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one or multiple of these.compute_nsize
Download VCF file and its index file from Open GWASdownload_vcf
Search Open GWAS for datasets matching criteriafind_sumstats
Check that summary statistics from GWAS are in a homogeneous formatformat_sumstats
Formatted exampleformatted_example
Get combinations of uncorrected allele and effect (and frq) columnsget_eff_frq_allele_combns
Infer genome buildsget_genome_builds
UCSC Chain file hg19 to hg38hg19ToHg38
UCSC Chain file hg38 to hg19hg38ToHg19
Local ieu-a-298 file from IEU Open GWASieu-a-298
Import full genome-wide GWAS summary statistics from Open GWASimport_sumstats
Tabix-index file: tableindex_tabular
Infer if effect relates to a1 or A2 if ambiguously namedinfer_effect_column
Genome build liftoverliftover
List munged summary statisticslist_sumstats
Load the reference genome data for SNPs of interestload_ref_genome_data
Loads the SNP locations and alleles for Homo sapiens from dbSNP buildsload_snp_loc_data
Parse data from log filesparse_logs
GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subsetraw_ALSvcf
GWAS Educational Attainment Okbay 2016 - Subsetraw_eduAttainOkbay
Read in file headerread_header
Determine summary statistics file type and read them into memoryread_sumstats
Read in VCF fileread_vcf
Register coresregister_cores
Standardise the column headers in the Summary Statistics filesstandardise_header
Summary Statistics Column HeaderssumstatsColHeaders
VCF to DFvcf2df
Write sum stats file to diskwrite_sumstats