get_lastCDSUTR3: Extract the last unspliced region of each transcript

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Extract the last unspliced region of each transcript

Description

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.

Usage

get_lastCDSUTR3(
  TxDb = getInPASTxDb(),
  genome = getInPASGenome(),
  chr2exclude = getChr2Exclude(),
  outdir = getInPASOutputDirectory(),
  MAX_EXONS_GAP = 10000
)

Arguments

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. chrM and alternative scaffolds representing different haplotypes should be excluded.
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.

Value

A BED file with 6 columns: chr, chrStart, chrEnd, name, score, and strand.

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.