breakpointOverlaps: A function to extract the reads overlapping to fusion...
In chimera: A package for secondary analysis of fusion products

Description Usage Arguments Value Author(s) Examples

A function to extract the reads overlapping to fusion breakpoint.

1	breakpointOverlaps(fset, plot=FALSE, ylim=NULL)

`fset`	An fSet object. The slots fusionRNA and fusionGA needs to be loaded
`plot`	If FALSE plot is not printed
`ylim`	If NULL it uses the full fusion transcript coverage to define the ylim of the plot. If setted it can be used to zoom in the plot to better see the structure of the coverage at the brek point

An object of GAlignment class. A plot of the fusion trascript coverage in blue and of the reads spanning over the break point in yellow.

Raffaele A Calogero

load(paste(find.package(package="chimera"), "/examples/fset_ARFGEF2-SULF2.rda", sep=""))
my.seq <- chimeraSeqs(my.fset)
my.fset <- addRNA(my.fset, my.seq)
tmp <- breakpointOverlaps(my.fset)