prepareGTF: Prepare GTF file for use with plotGeneRegion

In fmicompbio/swissknife: Handy code shared in the FMI CompBio group

Prepare GTF file for use with plotGeneRegion

Description

This function sets the names of the transcript and gene ID columns of the gtf file to "transcript" and "gene", removes version tags of the transcripts/genes and retains only the "exon" entries. The purpose is to make the file amenable to plotting with Gviz, using the plotGeneRegion function.

Usage

prepareGTF(
  gtf,
  transcriptIdColumn = "transcript_id",
  geneIdColumn = "gene_id",
  geneSymbolColumn = "gene_name"
)

Arguments

gtf	Character scalar, path to gtf file (tested with Ensembl/Gencode files).
transcriptIdColumn	Character scalar, the column in the gtf file that contains the transcript ID.
geneIdColumn	Character scalar, the column in the gtf file that contains the gene ID.
geneSymbolColumn	Character scalar, the column in the gtf file that contains the gene symbol (if available). Set to "" if not available (in which case the gene IDs will be used in its place).

Author(s)

Charlotte Soneson

Examples

gtf <- prepareGTF(gtf = system.file("extdata/plotGeneRegion/mm10_ensembl98.gtf",
                                    package = "swissknife"))
                                    

fmicompbio/swissknife documentation built on June 11, 2025, 4:17 p.m.