VCFArray
Representing on-disk / remote VCF files as array-like objects
Bioconductor version: Release (3.20)
VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.
Author: Qian Liu [aut, cre], Martin Morgan [aut]
Maintainer: Qian Liu <qliu7 at buffalo.edu>
citation("VCFArray")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VCFArray")
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("VCFArray")| VCFArray: DelayedArray objects with on-disk/remote VCF backend | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Sequencing, Software, VariantAnnotation |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6), methods, BiocGenerics, DelayedArray(>= 0.7.28) |
| Imports | tools, GenomicRanges, VariantAnnotation(>= 1.29.3), GenomicFiles(>= 1.17.3), S4Vectors(>= 0.19.19), Rsamtools |
| System Requirements | |
| URL | https://github.com/Liubuntu/VCFArray |
| Bug Reports | https://github.com/Liubuntu/VCFArray/issues |
See More
| Suggests | SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown |
| 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 | VCFArray_1.22.0.tar.gz |
| Windows Binary (x86_64) | VCFArray_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | VCFArray_1.22.0.tgz |
| macOS Binary (arm64) | VCFArray_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VCFArray |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VCFArray |
| Bioc Package Browser | https://code.bioconductor.org/browse/VCFArray/ |
| Package Short Url | https://bioconductor.org/packages/VCFArray/ |
| Package Downloads Report | Download Stats |