plotCoverage {chimera} | R Documentation

## 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

### 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))

[Package chimera version 1.27.1 Index]