VCFArray

Representing on-disk / remote VCF files as array-like objects

Bioconductor version: 3.23 · Package version: 1.28.0

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

Installation

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

BiocManager::install("VCFArray")

Details

Maintainer	Qian Liu <qliu7@buffalo.edu>
Author	Qian Liu [aut, cre], Martin Morgan [aut]
License	GPL-3
URL	https://github.com/Liubuntu/VCFArray
Bug Reports	https://github.com/Liubuntu/VCFArray/issues
Downloads rank	504
Source branch	RELEASE_3_23
biocViews	DataRepresentation, Infrastructure, Sequencing, Software, VariantAnnotation

Documentation

VCFArray: DelayedArray objects with on-disk/remote VCF backend

Download

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

Source package	VCFArray_1.28.0.tar.gz
Windows binary (x86_64)	VCFArray_1.28.0.zip
macOS binary (arm64)	VCFArray_1.28.0.tgz
macOS binary (x86_64)	VCFArray_1.28.0.tgz

Dependencies

Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)

Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools

Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown