Get gene models from a remote or local FASTA file

Source: R/buildReferenceData.R

Get gene models from a remote or local FASTA file

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)
#> Got local file: /private/var/folders/2n/wsp2zcc13jz9g_my_jhrwjk40000gq/T/Rtmp7hAr10/temp_libpath979f7e058fd3/GenomicDistributions/extdata/C_elegans_cropped_example.fa.gz