filterTranscripts {ORFik}R Documentation

Filter transcripts by lengths

Description

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

Usage

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

Arguments

txdb

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

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.

longestPerGene

logical (TRUE), return only longest valid transcript per gene.

stopOnEmpty

logical TRUE, stop if no valid transcripts are found ?

Details

If a transcript does not have a trailer, then the length is 0, so they will be filtered out if you set minThreeUTR to 1. 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, since 0 does mean there must exist a column called utr3_len etc.

Value

a character vector of valid transcript names

Examples

gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file)
txNames <- filterTranscripts(txdb, minFiveUTR = 1, minCDS = 30,
                             minThreeUTR = 1)
loadRegion(txdb, "mrna")[txNames]
loadRegion(txdb, "5utr")[txNames]


[Package ORFik version 1.6.9 Index]