MungeSumstats

This is the released version of MungeSumstats; for the devel version, see MungeSumstats.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Standardise summary statistics from GWAS

Bioconductor version: Release (3.23)

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.

Author: Alan Murphy [aut, cre] ORCID: 0000-0002-2487-8753 , Brian Schilder [aut, ctb] ORCID: 0000-0001-5949-2191 , Nathan Skene [aut] ORCID: 0000-0002-6807-3180

Maintainer: Alan Murphy <alanmurph94 at hotmail.com>

Citation (from within R, enter citation("MungeSumstats")):

Alan Murphy, Brian Schilder, Nathan Skene. MungeSumstats: Standardise summary statistics from GWAS. doi:10.18129/B9.bioc.MungeSumstats, R package version 1.20.0, https://bioconductor.org/packages/MungeSumstats.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("MungeSumstats")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MungeSumstats")

docker	HTML	R Script
MungeSumstats	HTML	R Script
OpenGWAS	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome
Version	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	Artistic-2.0
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
System Requirements
URL	https://github.com/neurogenomics/MungeSumstats https://al-murphy.github.io/MungeSumstats/
Bug Reports	https://github.com/neurogenomics/MungeSumstats/issues

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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MungeSumstats_1.20.0.tar.gz
Windows Binary (x86_64)	MungeSumstats_1.19.5.zip (64-bit only)
macOS Binary (big-sur-x86_64)	MungeSumstats_1.19.5.tgz
macOS Binary (sonoma-arm64)	MungeSumstats_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MungeSumstats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MungeSumstats
Package Short Url	https://bioconductor.org/packages/MungeSumstats/
Package Downloads Report	Download Stats