VariantExperiment
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment.
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
Bioconductor version: 3.10
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("VariantExperiment")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VariantExperiment")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VariantExperiment")| VariantExperiment-class | HTML | R Script |
| VariantExperiment-methods | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6.0), S4Vectors(>= 0.21.24), SummarizedExperiment(>= 1.13.0), GenomicRanges, GDSArray(>= 1.3.0), DelayedDataFrame(>= 1.0.0) |
| Imports | tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges |
| System Requirements | |
| URL | https://github.com/Bioconductor/VariantExperiment |
| Bug Reports | https://github.com/Bioconductor/VariantExperiment/issues |
See More
| Suggests | testthat, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VariantExperiment_1.0.0.tar.gz |
| Windows Binary | VariantExperiment_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | VariantExperiment_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VariantExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VariantExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/VariantExperiment/ |
| Package Short Url | https://bioconductor.org/packages/VariantExperiment/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |