getChromSizesFromFasta: Get gene models from a remote or local FASTA file

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Get gene models from a remote or local FASTA file

Description

Get gene models from a remote or local FASTA file

Usage

getChromSizesFromFasta(source, destDir = NULL, convertEnsemblUCSC = FALSE)

Arguments

source	a string that is either a path to a local or remote FASTA
destDir	a string that indicates the path to the directory where the downloaded FASTA file should be stored
convertEnsemblUCSC	a logical indicating whether Ensembl style chromosome annotation should be changed to UCSC style (add chr)

Value

a named vector of sequence lengths

Examples

CElegansFasteCropped = system.file("extdata", 
                                   "C_elegans_cropped_example.fa.gz", 
                                   package="GenomicDistributions")
CElegansChromSizes = getChromSizesFromFasta(CElegansFasteCropped)

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.