txNamesWithLeaders {ORFik} | R Documentation |
Filter transcripts to those whohave 5' UTR, CDS, 3' UTR of some lengths, pick the longest per gene.
txNamesWithLeaders(txdb, minFiveUTR = 30L, minCDS = 150L, minThreeUTR = 30L)
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 |
a character vector of valid tramscript names
gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik") txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file, format = "gtf") txNames <- txNamesWithLeaders(txdb)