VariantExperiment
This is the released version of VariantExperiment; for the devel version, see VariantExperiment.
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
Bioconductor version: Release (3.23)
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("VariantExperiment")):Qian Liu, Hervé Pagès, Martin Morgan. VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend. doi:10.18129/B9.bioc.VariantExperiment, R package version 1.26.0, https://bioconductor.org/packages/VariantExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 |
See More
| Suggests | testthat, knitr, rmarkdown, markdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VariantExperiment_1.26.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |