modPlot: visualize a gene model

In genomicsclass/ph525x: support functions and data for edX course PH525

visualize a gene model

Description

visualize a gene model from a resource that can be processed via GeneRegionTrack in Gviz

Usage

modPlot(symbol, genome = "hg19", annoResource = Homo.sapiens, getter = exonsBy, byattr = "gene", expansion = 0, collapseTranscripts = "meta", useGeneSym = TRUE, plot.it = TRUE, ...)

Arguments

symbol	gene symbol resolvable in annoResource
genome	character tag
annoResource	OrganismDb or TxDb instance
getter	exon GRanges generator
byattr	value of "by" argument to getter
expansion	numeric, number of bp upstream and downstream of gene region to include
collapseTranscripts	if TRUE a single gene model is provided; if FALSE all transcripts displayed separately
useGeneSym	if TRUE each transcript labeled with gene symbol, if FALSE, UCSC labels are used
plot.it	if TRUE plotTracks is run, if FALSE, Gviz track object is returned
...	passed to plotTracks

Details

In cases of overlapping gene regions, transcript information from another gene may appear in the plot.

Value

depends on value of plot.it

Examples

modPlot("NISCH", collapse=FALSE, useGeneSym=FALSE)

genomicsclass/ph525x documentation built on July 16, 2022, 1:37 p.m.