txmodels {TxRegInfra}R Documentation

use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation

Description

use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation

Usage

txmodels(sym, gr, edb = "EnsDb.Hsapiens.v75", plot.it = FALSE,
  radius = 0, ...)

Arguments

sym

a gene symbol to be looked up in biovizBase::genesymbol table

gr

a GRanges instance, anticipated to be length 1

edb

a character(1) name of an EnsDb annotation package

plot.it

a logical(1) specifying whether Gviz::plotTracks should be run

radius

a numeric(1) specifying number to add to IRanges instance used to subset gene models from ensembldb::exonsBy output

...

passed to Gviz::GeneRegionTrack

Value

an instance of Gviz::GeneRegionTrack, invisibly returned

Examples

t0 = txmodels('ORMDL3', plot.it=TRUE, name='ORMDL3')
t1 = txmodels('ORMDL3', plot.it=FALSE, name='meta', collapseTranscripts='meta')
requireNamespace('Gviz')
Gviz::plotTracks(list(Gviz::GenomeAxisTrack(), t0, t1), showId=TRUE)

[Package TxRegInfra version 1.10.0 Index]