MungeSumstats
Standardise summary statistics from GWAS
Bioconductor version: 3.24 · Package version: 1.21.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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
| Maintainer | Alan Murphy <alanmurph94@hotmail.com> |
| Author | Alan 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>) |
| License | Artistic-2.0 |
| URL | https://github.com/neurogenomics/MungeSumstats, https://al-murphy.github.io/MungeSumstats/ |
| Bug Reports | https://github.com/neurogenomics/MungeSumstats/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ComparativeGenomics, Genetics, GenomeWideAssociation, GenomicVariation, Preprocessing, SNP, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/MungeSumstats/ |
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 1.21.0, https://bioconductor.org/packages/MungeSumstats.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | MungeSumstats_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