VariantExperiment
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
Bioconductor version: 3.23 · Package version: 1.26.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantExperiment")Details
| Maintainer | Qian Liu <Qian.Liu@roswellpark.org> |
| Author | Qian Liu [aut, cre], Hervé Pagès [aut], Martin Morgan [aut] |
| License | GPL-3 |
| URL | https://github.com/Bioconductor/VariantExperiment |
| Bug Reports | https://github.com/Bioconductor/VariantExperiment/issues |
| Downloads rank | 185 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software |
Documentation
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Dependencies
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