This is the development version of VariantExperiment; for the stable release version, see VariantExperiment.
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS BackendBioconductor version: Development (3.22)
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, entercitation("VariantExperiment")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("VariantExperiment")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VariantExperiment")Follow Installation instructions to use this package in your R session.
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