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isoform2longest

Source: R/isoform2longest.R
isoform2longest.Rd

This function extracts the longest isoform from either NCBI or ENSEMBL CDS input.

Usage

isoform2longest(cds, source = "NCBI")

Arguments

cds

DNAStringSet [mandatory]

source

source indicating either NCBI, ENSEMBL or WORMBASE [default: NCBI]

Value

DNAStringSet

See also

XStringSet-class

Author

Kristian K Ullrich

Examples

if (FALSE) { # \dontrun{
## load example sequence data
## set NCBI URL
NCBI <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/"
HOMSAP.NCBI.cds.url <- paste0(NCBI,
    "GCF/000/001/405/GCF_000001405.39_GRCh38.p13/",
    "GCF_000001405.39_GRCh38.p13_cds_from_genomic.fna.gz")
HOMSAP.NCBI.cds.file <- tempfile()
## download CDS file
download.file(HOMSAP.NCBI.cds.url, HOMSAP.NCBI.cds.file, quiet=FALSE)
HOMSAP.NCBI.cds <- Biostrings::readDNAStringSet(HOMSAP.NCBI.cds.file)
## get longest isoform
HOMSAP.NCBI.cds.longest <- isoform2longest(HOMSAP.NCBI.cds, "NCBI")
length(HOMSAP.NCBI.cds)
length(HOMSAP.NCBI.cds.longest)
## set ENSEMBL URL
ensembl <- "ftp://ftp.ensembl.org/pub/release-101/fasta/"
## set Homo sapiens CDS URL
HOMSAP.ENSEMBL.cds.url <- paste0(ensembl,
    "homo_sapiens/cds/Homo_sapiens.GRCh38.cds.all.fa.gz")
HOMSAP.ENSEMBL.cds.file <- tempfile()
## download CDS file
download.file(HOMSAP.ENSEMBL.cds.url, HOMSAP.ENSEMBL.cds.file, quiet=FALSE)
HOMSAP.ENSEMBL.cds <- Biostrings::readDNAStringSet(HOMSAP.ENSEMBL.cds.file)
## get longest isoform
HOMSAP.ENSEMBL.cds.longest<-isoform2longest(HOMSAP.ENSEMBL.cds, "ENSEMBL")
length(HOMSAP.ENSEMBL.cds)
length(HOMSAP.ENSEMBL.cds.longest)
} # }