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

Description Usage Arguments Value Examples

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

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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

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#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 21, 2021, 4:15 a.m.