VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

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.

Package details

AuthorQian Liu [aut, cre], Hervé Pagès [aut], Martin Morgan [aut]
Bioconductor views Annotation DataRepresentation GenomeAnnotation GenotypingArray Infrastructure Sequencing
MaintainerQian Liu <Qian.Liu@roswellpark.org>
LicenseGPL-3
Version1.2.0
URL https://github.com/Bioconductor/VariantExperiment
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("VariantExperiment")

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VariantExperiment documentation built on April 29, 2020, 6 a.m.