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 (3.14)

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 removes duplicates across SNPs.

Author: Alan Murphy [aut, cre] , Brian Schilder [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 "4.1") and enter:

if (!requireNamespace("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

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

browseVignettes("MungeSumstats")

 

HTML R Script OpenGWAS
HTML R Script Standardise the format of summary statistics from GWAS with MungeSumstats
PDF   Reference Manual
Text   NEWS

Details

biocViews ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome
Version 1.1.4
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License Artistic-2.0
Depends R (>= 4.1)
Imports magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, BSgenome, Biostrings, VariantAnnotation, stringr, googleAuthR, httr, jsonlite, methods
LinkingTo
Suggests SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, IRanges, GenomeInfoDb, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr
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_1.1.4.tar.gz
Windows Binary MungeSumstats_1.1.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) MungeSumstats_1.1.4.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: