refGenome (version 1.7.7)

addIsCoding: Add information on coding/non-coding status.

Description

The addIsCoding method extracts positions from 'CDS' features in the ensemblGenome object. The positions of the 'CDS' features are compared with the splice-junction positions in the ensemblJunctions object. When a match is found, the splice junction is marked as coding, otherwise the junction is marked as non-coding. The coding information is calculated for each flanking exon of the splice-junction. The column name for the left side (lend) is licd, the name for the right side (rstart) is ricd.

Usage

addIsCoding(object,ens)

Arguments

object

ensemblJunctions. The object to which isCoding columns are added.

ens

ensemblGenome. Genome object which should contain 'CDS' features.

Examples

# NOT RUN {
ef <- system.file("extdata", "hs.ensembl.62.small.RData", package="refGenome")
ens <- loadGenome(ef)
enj <- getSpliceTable(ens)
addIsCoding(enj, ens)
# }