Package: PlinkMatrix 1.1.0

Vince Carey

PlinkMatrix: DelayedArray interface for plink bed files

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.

Authors:Vince Carey [aut, cre], NHGRI U24HG004059 [fnd]

PlinkMatrix_1.1.0.tar.gz
PlinkMatrix_1.1.0.zip(r-4.7)PlinkMatrix_1.1.0.zip(r-4.6)PlinkMatrix_1.1.0.zip(r-4.5)
PlinkMatrix_1.1.0.tgz(r-4.6-x86_64)PlinkMatrix_1.1.0.tgz(r-4.6-arm64)PlinkMatrix_1.1.0.tgz(r-4.5-x86_64)PlinkMatrix_1.1.0.tgz(r-4.5-arm64)
PlinkMatrix_1.1.0.tar.gz(r-4.7-arm64)PlinkMatrix_1.1.0.tar.gz(r-4.7-x86_64)PlinkMatrix_1.1.0.tar.gz(r-4.6-arm64)PlinkMatrix_1.1.0.tar.gz(r-4.6-x86_64)
PlinkMatrix_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PlinkMatrix/json (API)

# Install 'PlinkMatrix' in R:

install.packages('PlinkMatrix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/plinkmatrix/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

example_GRanges - Sample GRanges coordinated with example_PlinkMatrix
g445samples - Sample characteristics of 445 GEUVADIS samples

On BioConductor:PlinkMatrix-1.1.0(bioc 3.24)PlinkMatrix-1.0.0(bioc 3.23)

infrastructure genetics cpp

4.70 score 1 stars 10 scripts 9 exports 54 dependencies

Last updated from:bfa6bf0243. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	181
linux-devel-arm64	NOTE	283
linux-devel-x86_64	NOTE	329
source / vignettes	OK	266
linux-release-arm64	NOTE	363
linux-release-x86_64	NOTE	343
macos-release-arm64	NOTE	172
macos-release-x86_64	NOTE	409
macos-oldrel-arm64	NOTE	215
macos-oldrel-x86_64	NOTE	306
windows-devel	NOTE	293
windows-release	NOTE	245
windows-oldrel	NOTE	207
wasm-release	OK	159

Exports:example_PlinkMatrix get_plink_example_path getSampleData getVariantData plid2gr PlinkMatrix PlinkSeed read_bed_subset show

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob cachem cli cpp11 curl DBI dbplyr DelayedArray dplyr fastmap filelock generics GenomicRanges glue httr2 IRanges lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R6 rappdirs Rcpp rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector

PlinkMatrix: DelayedArray interface to plink bed-type files

Rendered fromPlinkMatrix.Rmdusingknitr::rmarkdown

Last update: 2026-04-06
Started: 2026-02-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Method: dim for delayed plink	dim,PlinkSeed-method
Method: dimnames for delayed plink	dimnames,PlinkSeed-method
sample GRanges coordinated with example_PlinkMatrix	example_GRanges
produce PlinkMatrix from example data	example_PlinkMatrix
sample characteristics of 445 GEUVADIS samples	g445samples
operate with BiocFileCache to retrieve zip file of plink example data	get_plink_example_path
Get sample metadata	getSampleData
Get variant metadata	getVariantData
produce GRanges from variant notation for plink example from geuvadis	plid2gr
Constructor for DelayedArray	PlinkMatrix
Delayed interface to Plink genotype files	PlinkMatrix-pkg
read subset for use in delayed matrix approach	read_bed_subset
present seed concisely	show,PlinkSeed-method