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alabaster.vcf

Save and Load Variant Data to/from File


Bioconductor version: Release (3.18)

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("alabaster.vcf")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("alabaster.vcf")

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("alabaster.vcf")
Saving and loading VCFs HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews DataImport, DataRepresentation, Software
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends alabaster.base, VariantAnnotation
Imports methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, testthat
Linking To
Enhances
Depends On Me
Imports Me alabaster
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package alabaster.vcf_1.2.0.tar.gz
Windows Binary alabaster.vcf_1.2.0.zip
macOS Binary (x86_64) alabaster.vcf_1.2.0.tgz
macOS Binary (arm64) alabaster.vcf_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/alabaster.vcf
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/alabaster.vcf
Bioc Package Browser https://code.bioconductor.org/browse/alabaster.vcf/
Package Short Url https://bioconductor.org/packages/alabaster.vcf/
Package Downloads Report Download Stats