VCFArray

DOI: 10.18129/B9.bioc.VCFArray    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	VCFArray: DelayedArray objects with on-disk/remote VCF backend
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Sequencing, Software, VariantAnnotation
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 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
LinkingTo
Suggests	SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/Liubuntu/VCFArray
BugReports	https://github.com/Liubuntu/VCFArray/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	VCFArray_1.8.0.tar.gz
Windows Binary	VCFArray_1.8.0.zip
macOS 10.13 (High Sierra)	VCFArray_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VCFArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VCFArray
Package Short Url	https://bioconductor.org/packages/VCFArray/
Package Downloads Report	Download Stats