View source: R/00.get_lastCDSUTR3.R
get_lastCDSUTR3 | R Documentation |
Extract the last unspliced region of each transcript from a TxDb. These regions could be the last 3'UTR exon for transcripts whose 3' UTRs are composed of multiple exons or last CDS regions and 3'UTRs for transcripts whose 3'UTRs and last CDS regions are on the same single exon.
get_lastCDSUTR3( TxDb = getInPASTxDb(), genome = getInPASGenome(), chr2exclude = getChr2Exclude(), outdir = getInPASOutputDirectory(), MAX_EXONS_GAP = 10000 )
TxDb |
An object of GenomicFeatures::TxDb |
genome |
An object of BSgenome::BSgenome |
chr2exclude |
A character vector, NA or NULL, specifying chromosomes or
scaffolds to be excluded for InPAS analysis. |
outdir |
A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created. |
MAX_EXONS_GAP |
An integer(1) vector, maximal gap sizes between the last known CP sites to a nearest downstream exon. Default is 10 kb for mammalian genomes. For other species, user need to adjust this parameter. |
A BED file with 6 columns: chr, chrStart, chrEnd, name, score, and strand.
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