plotTranscriptsFromUCSC: Plot transcripts directly from UCSC OrgDb and TxDb objects.

In kauralasoo/wiggleplotr: Make read coverage plots from BigWig files

Plot transcripts directly from UCSC OrgDb and TxDb objects.

Description

A wrapper around the plotTranscripts function. See the documentation for (plotTranscripts) for more information. Note that this function is much slower than (plotTranscripts) or (plotTranscriptsFromEnsembldb) functions, because indivudally extracting exon coordinates from txdb objects is quite inefficient.

Usage

plotTranscriptsFromUCSC(orgdb, txdb, gene_names, transcript_ids = NULL, ...)

Arguments

orgdb	UCSC OrgDb object.
txdb	UCSC TxDb obejct.
gene_names	List of gene genaes to be plot.
transcript_ids	Optional list of transcript ids to be plot. (default = NULL)
...	Additional parameters to be passed to plotTranscripts

Value

Transcript plot.

Examples

#Load OrgDb and TxDb objects with UCSC gene annotations
require("org.Hs.eg.db")
require("TxDb.Hsapiens.UCSC.hg38.knownGene")
orgdb = org.Hs.eg.db
txdb = TxDb.Hsapiens.UCSC.hg38.knownGene

plotTranscriptsFromUCSC(orgdb, txdb, "NCOA7", transcript_ids = c("ENST00000438495.6", "ENST00000368357.7"))

kauralasoo/wiggleplotr documentation built on July 4, 2022, 11:43 a.m.