cds2genepos: cds2genepos

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

cds2genepos

Description

This function extracts the gene position from either NCBI or ENSEMBL CDS input.

Usage

cds2genepos(cds, source = "NCBI", keep.names = NULL)

Arguments

cds	DNAStringSet [mandatory]
source	source indicating either NCBI or ENSEMBL [default: NCBI]
keep.names	vector indicating gene ids to be kept before chromosomal position assignment [default: NULL]

Value

matrix 1: $gene.seq.id
2: $gene.chr
3: $gene.start
4: $gene.end
5: $gene.mid
6: $gene.strand
7: $gene.idx

Author(s)

Kristian K Ullrich

See Also

isoform2longest

Examples

## load example sequence data
data("ath", package="CRBHits")
ath.genepos <- cds2genepos(
    cds=ath,
    source="ENSEMBL")
## Not run: 
## load example sequence data
## set EnsemblPlants URL
ensemblPlants <- "ftp://ftp.ensemblgenomes.org/pub/plants/release-48/fasta/"
## set Arabidopsis thaliana CDS URL
ARATHA.cds.url <- paste0(ensemblPlants,
    "arabidopsis_thaliana/cds/Arabidopsis_thaliana.TAIR10.cds.all.fa.gz")
ARATHA.cds.file <- tempfile()
## download CDS
download.file(ARATHA.cds.url, ARATHA.cds.file, quiet=FALSE)
ARATHA.cds <- Biostrings::readDNAStringSet(ARATHA.cds.file)
## get gene position
ARATHA.cds.genepos <- cds2genepos(ARATHA.cds, "ENSEMBL")

## End(Not run)

kullrich/CRBHits documentation built on March 29, 2024, 11:34 a.m.