isoform2longest: isoform2longest

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

isoform2longest

Description

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

Author(s)

Kristian K Ullrich

See Also

XStringSet-class

Examples

## Not run: 
## 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)

## End(Not run)

kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.