VariantExperiment
This is the development version of VariantExperiment; for the stable release version, see VariantExperiment.
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataRepresentation, GenomeAnnotation, GenotypingArray, Infrastructure, Sequencing, Software |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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, DelayedArray, Biostrings, IRanges |
| System Requirements | |
| URL | https://github.com/Bioconductor/VariantExperiment |
| Bug Reports | https://github.com/Bioconductor/VariantExperiment/issues |
See More
| Suggests | testthat, knitr, rmarkdown, markdown, BiocStyle |
| 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |