filterTranscripts {ORFik}R Documentation

Get the transcripts with accepted lengths of leaders, cds and trailer.

Description

Filter transcripts to those who have leaders, CDS, trailers of some lengths, pick the longest per gene.

Usage

filterTranscripts(txdb, minFiveUTR = 30L, minCDS = 150L,
  minThreeUTR = 30L, stopOnEmpty = TRUE)

Arguments

txdb

a TxDb file or a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite)

minFiveUTR

(integer) minimum bp for 5' UTR during filtering for the transcripts. Set to NULL if no 5' UTRs exists for annotation.

minCDS

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

minThreeUTR

(integer) minimum bp for 3' UTR during filtering for the transcripts. Set to NULL if no 3' UTRs exists for annotation.

stopOnEmpty

logical TRUE, stop if no valid names are found ?

Details

If a transcript does not have a trailer, then the length is 0, so they will be filtered out. So only transcripts with leaders, cds and trailers will be returned. You can set the integer to 0, that will return all within that group.

If your annotation does not have leaders or trailers, set them to NULL.

Value

a character vector of valid tramscript names

Examples

gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file)
txNames <- filterTranscripts(txdb)


[Package ORFik version 1.4.0 Index]