PlinkMatrix

DelayedArray interface for plink bed files

Bioconductor version: 3.23 · Package version: 1.0.0

This package provides a DelayedArray interface for plink bed files. There is support for interfacing to plink genotype data via RangedSummarizedExperiment. Example data from the GEUVADIS project (internationalgenome.org) are used for demonstration.

Installation

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

BiocManager::install("PlinkMatrix")

Details

Maintainer	Vince Carey <stvjc@channing.harvard.edu>
Author	Vince Carey [aut, cre] (ORCID: <https://orcid.org/0000-0003-4046-0063>), NHGRI U24HG004059 [fnd]
License	MIT + file LICENSE
URL	https://github.com/vjcitn/PlinkMatrix
Bug Reports	https://github.com/vjcitn/PlinkMatrix/issues
Downloads rank	199
Source branch	RELEASE_3_23
biocViews	Genetics, Infrastructure, Software

Documentation

PlinkMatrix: DelayedArray interface to plink bed-type files

Download

Follow the installation instructions to use this package in your R session.

Source package	PlinkMatrix_1.0.0.tar.gz
Windows binary (x86_64)	PlinkMatrix_1.0.0.zip
macOS binary (arm64)	PlinkMatrix_1.0.0.tgz
macOS binary (x86_64)	PlinkMatrix_1.0.0.tgz

Dependencies

Depends: R (>= 4.1.0), methods, Rcpp, DelayedArray, SummarizedExperiment

Imports: BiocFileCache, GenomicRanges, IRanges

LinkingTo: Rcpp

Suggests: knitr, BiocStyle, testthat, rmarkdown, irlba, GenomeInfoDb