MungeSumstats

DOI: 10.18129/B9.bioc.MungeSumstats  

Standardise summary statistics from GWAS

Bioconductor version: Release (3.16)

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] , Brian Schilder [aut, ctb] , Nathan Skene [aut]

Maintainer: Alan Murphy <alanmurph94 at hotmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer, RCurl
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/neurogenomics/MungeSumstats
BugReports	https://github.com/neurogenomics/MungeSumstats/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MungeSumstats_1.6.0.tar.gz
Windows Binary	MungeSumstats_1.6.0.zip
macOS Binary (x86_64)	MungeSumstats_1.6.0.tgz
macOS Binary (arm64)	MungeSumstats_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MungeSumstats
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MungeSumstats
Bioc Package Browser	https://code.bioconductor.org/browse/MungeSumstats/
Package Short Url	https://bioconductor.org/packages/MungeSumstats/
Package Downloads Report	Download Stats