loadTranscriptType {ORFik}R Documentation

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(path, part = "rRNA", tx = NULL)

Arguments

path

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), add to save run time.

Value

a GRangesList of transcript of that type

References

doi: 10.1002/0471250953.bi0410s25


[Package ORFik version 1.6.9 Index]