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MungeSumstats

Standardise summary statistics from GWAS

Bioconductor version: 3.24 · Package version: 1.21.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MungeSumstats")

Details

MaintainerAlan Murphy <alanmurph94@hotmail.com>
AuthorAlan Murphy [aut, cre] (ORCID: <https://orcid.org/0000-0002-2487-8753>), Brian Schilder [aut, ctb] (ORCID: <https://orcid.org/0000-0001-5949-2191>), Nathan Skene [aut] (ORCID: <https://orcid.org/0000-0002-6807-3180>)
LicenseArtistic-2.0
URLhttps://github.com/neurogenomics/MungeSumstats, https://al-murphy.github.io/MungeSumstats/
Bug Reportshttps://github.com/neurogenomics/MungeSumstats/issues
Downloads rank984
Source branchdevel
biocViewsComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome

Download

Follow the installation instructions to use this package in your R session.

Source packageMungeSumstats_1.21.0.tar.gz
macOS binary (arm64)MungeSumstats_1.21.0.tgz
macOS binary (x86_64)MungeSumstats_1.21.0.tgz
Dependencies

Depends: R (>= 4.1)

Imports: data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, IRanges, ieugwasr (>= 1.0.1), BSgenome, Biostrings, stringr, VariantAnnotation, methods, parallel, rtracklayer (>= 1.59.1), RCurl

Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles