chimera (version 1.14.0)

plotCoverage: A function to plot the coverage of a fusion gene

Description

A function to plot the coverage of a fusion gene.

Usage

plotCoverage(fset, plot.type=c("exons","junctions"), junction.spanning=20, fusion.only=FALSE, xlab="nts", ylab="Coverage", main="", col.box1="red", col.box2="green", ybox.lim=c(-4,-1))

Arguments

fset

A fSet object

plot.type

exons plot exons coverage as junctions plot coverage of junction between exons

junction.spanning

number of nucleotides located upstream and downstream the junction/fusion location

fusion.only

if TRUE only fusion coverage is plotted

xlab

x-axis label

ylab

y-axis label

main

Plot title

col.box1

color of the box describing the first gene

col.box2

color of the box describing the second gene

ybox.lim

y range defining the height of the box representing the exons

See Also

fusionName, chimeraSeqs

Examples

	tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19")
	fusion.names <- fusionName(tmp)
	fusion.names
	myset <- tmp[[13]]
	trs <- chimeraSeqs(myset, type="transcripts")
	myset <- addRNA(myset , trs)
	tmp.seq <- fusionRNA(myset)
	myset <- addGA(myset, paste(path.package(package="chimera"),"/examples/mcf7_trs_accepted_hits.bam",sep=""))
	ga <- fusionGA(myset)
	plotCoverage(myset, plot.type="exons", col.box1="red", col.box2="green", ybox.lim=c(-4,-1))
	plotCoverage(myset, plot.type="junctions", col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1))
	plotCoverage(myset, fusion.only=TRUE, col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1))