VariantExperiment

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")

VariantExperiment-class	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software
Version	1.18.1
In Bioconductor since	BioC 3.10 (R-3.6) (5 years)
License	GPL-3
Depends	R (>= 3.6.0), S4Vectors(>= 0.21.24), SummarizedExperiment(>= 1.13.0), GenomicRanges
Imports	GDSArray(>= 1.11.1), DelayedDataFrame(>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, DelayedArray, Biostrings, IRanges
System Requirements
URL	https://github.com/Bioconductor/VariantExperiment
Bug Reports	https://github.com/Bioconductor/VariantExperiment/issues

Suggests	testthat, knitr, rmarkdown, markdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	VariantExperiment_1.18.1.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/VariantExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VariantExperiment
Bioc Package Browser	https://code.bioconductor.org/browse/VariantExperiment/
Package Short Url	https://bioconductor.org/packages/VariantExperiment/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.19	Source Archive