txNamesWithLeaders {ORFik}R Documentation

Get the transcripts that have minimum lengths of leaders and cds.

Description

Filter transcripts to those whohave 5' UTR, CDS, 3' UTR of some lengths, pick the longest per gene.

Usage

txNamesWithLeaders(txdb, minFiveUTR = 30L, minCDS = 150L,
  minThreeUTR = 30L)

Arguments

txdb

a TxDb object from gtf

minFiveUTR

(integer) minimum bp for 5' UTR during filtering for the transcripts

minCDS

(integer) minimum bp for CDS during filtering for the transcripts

minThreeUTR

(integer) minimum bp for 3' UTR during filtering for the transcripts

Value

a character vector of valid tramscript names

Examples

gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file, format = "gtf")
txNames <- txNamesWithLeaders(txdb)
[Package ORFik version 1.0.0 Index]