Bioconductor/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.

Getting started

Package details

Bioconductor views Annotation DataRepresentation GenomeAnnotation GenotypingArray Infrastructure Sequencing
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor/VariantExperiment documentation built on May 1, 2022, 8:45 a.m.