DOI: 10.18129/B9.bioc.VariantExperiment    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment.

A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

Bioconductor version: 3.14

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>

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biocViews Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.10 (R-3.6) (2.5 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, SeqVarTools, DelayedArray, Biostrings, IRanges
Suggests testthat, knitr, rmarkdown, markdown
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