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

In chimera: A package for secondary analysis of fusion products

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

Author(s)

Raffaele A Calogero

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))

chimera documentation built on Nov. 8, 2020, 5:16 p.m.