PlinkMatrix
This is the released version of PlinkMatrix; for the devel version, see PlinkMatrix.
DelayedArray interface for plink bed files
Bioconductor version: Release (3.23)
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.
Author: Vince Carey [aut, cre]
, NHGRI U24HG004059 [fnd]
Maintainer: Vince Carey <stvjc at channing.harvard.edu>
citation("PlinkMatrix")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PlinkMatrix")
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("PlinkMatrix")| PlinkMatrix: DelayedArray interface to plink bed-type files | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Genetics, Infrastructure, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0), methods, Rcpp, DelayedArray, SummarizedExperiment |
| Imports | BiocFileCache, GenomicRanges, IRanges |
| System Requirements | |
| URL | https://github.com/vjcitn/PlinkMatrix |
| Bug Reports | https://github.com/vjcitn/PlinkMatrix/issues |
See More
| Suggests | knitr, BiocStyle, testthat, rmarkdown, irlba, GenomeInfoDb |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (big-sur-x86_64) | PlinkMatrix_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | PlinkMatrix_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PlinkMatrix |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PlinkMatrix |
| Bioc Package Browser | https://code.bioconductor.org/browse/PlinkMatrix/ |
| Package Short Url | https://bioconductor.org/packages/PlinkMatrix/ |
| Package Downloads Report | Download Stats |