MungeSumstats

DOI: 10.18129/B9.bioc.MungeSumstats    

This is the development version of MungeSumstats; for the stable release version, see MungeSumstats.

Standardise summary statistics from GWAS

Bioconductor version: Development (3.17)

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>

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

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MungeSumstats")

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

Documentation

PDF   Reference Manual

Details

biocViews ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome
Version 1.7.8
In Bioconductor since BioC 3.13 (R-4.1) (1.5 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
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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