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VCFArray

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


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews DataRepresentation, Infrastructure, Sequencing, Software, VariantAnnotation
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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
See More
Suggests SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
Linking To
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Package Archives

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

Source Package VCFArray_1.18.0.tar.gz
Windows Binary VCFArray_1.18.0.zip
macOS Binary (x86_64) VCFArray_1.18.0.tgz
macOS Binary (arm64) VCFArray_1.18.0.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/
Package Downloads Report Download Stats