VariantExperiment

DOI: 10.18129/B9.bioc.VariantExperiment    

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Bioconductor version: Release (3.11)

VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.

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

Maintainer: Qian Liu <Qian.Liu at roswellpark.org>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("VariantExperiment")

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("VariantExperiment")

 

HTML	R Script	VariantExperiment-class
HTML	R Script	VariantExperiment-methods
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	GPL-3
Depends	R (>= 3.6.0), S4Vectors(>= 0.21.24), SummarizedExperiment(>= 1.13.0), GenomicRanges, GDSArray(>= 1.3.0), DelayedDataFrame(>= 1.0.0)
Imports	tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges
LinkingTo
Suggests	testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/Bioconductor/VariantExperiment
BugReports	https://github.com/Bioconductor/VariantExperiment/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	VariantExperiment_1.2.0.tar.gz
Windows Binary	VariantExperiment_1.2.0.zip
macOS 10.13 (High Sierra)	VariantExperiment_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VariantExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantExperiment
Package Short Url	https://bioconductor.org/packages/VariantExperiment/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive