loadTranscriptType: Load transcripts of given biotype

In JokingHero/ORFik: Open Reading Frames in Genomics

Load transcripts of given biotype

Description

Like rRNA, snoRNA etc. NOTE: Only works on gtf/gff, not .db object for now. Also note that these anotations are not perfect, some rRNA annotations only contain 5S rRNA etc. If your gtf does not contain evertyhing you need, use a resource like repeatmasker and download a gtf: https://genome.ucsc.edu/cgi-bin/hgTables

Usage

loadTranscriptType(object, part = "rRNA", tx = NULL)

Arguments

object	a TxDb, ORFik experiment or path to gtf/gff,
part	a character, default rRNA. Can also be: snoRNA, tRNA etc. As long as that biotype is defined in the gtf.
tx	a GRangesList of transcripts (Optional, default NULL, all transcript of that type), else it must be names a list to subset on.

Value

a GRangesList of transcript of that type

References

doi: 10.1002/0471250953.bi0410s25

Examples

gtf <- "path/to.gtf"
#loadTranscriptType(gtf, part = "rRNA")
#loadTranscriptType(gtf, part = "miRNA")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.