VCFArray

This is the released version of VCFArray; for the devel version, see VCFArray.

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

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DOI: 10.18129/B9.bioc.VCFArray

Bioconductor version: Release (3.22)

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.

Author: Qian Liu [aut, cre], Martin Morgan [aut]

Maintainer: Qian Liu <qliu7 at buffalo.edu>

Citation (from within R, enter citation("VCFArray")):

Installation

To install this package, start R (version "4.5") and enter:


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

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("VCFArray")

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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Sequencing, Software, VariantAnnotation

Version 1.26.0

In Bioconductor since BioC 3.9 (R-3.6) (6.5 years)

License GPL-3

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

System Requirements

URL https://github.com/Liubuntu/VCFArray

Bug Reports https://github.com/Liubuntu/VCFArray/issues

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

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package VCFArray_1.26.0.tar.gz

Windows Binary (x86_64) VCFArray_1.25.0.zip

macOS Binary (x86_64) VCFArray_1.26.0.tgz

macOS Binary (arm64) VCFArray_1.26.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/VCFArray

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VCFArray

Bioc Package Browser https://code.bioconductor.org/browse/VCFArray/

Package Short Url https://bioconductor.org/packages/VCFArray/

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