VCFArray

DOI: 10.18129/B9.bioc.VCFArray    

This is the development version of VCFArray; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("VCFArray", version = "3.9")

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 0.99.18
In Bioconductor since BioC 3.9 (R-3.6)
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 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_0.99.18.tar.gz
Windows Binary VCFArray_0.99.18.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) VCFArray_0.99.18.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 http://bioconductor.org/packages/VCFArray/
Package Downloads Report Download Stats

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