chimera (version 1.14.0)

supportingReads: A function to extract supporting reads values from a list of fSet object

Description

A function extracting supporting reads values from a list of fSet objects. Please note that not all outputs of supported tools provides both spanning reads, i.e. pair-end reads having one of the two mates spanning over the break point, and encompassing reads, i.e. pair-end reads having the two mates mapping on the exons of the two transcripts involved in the fusion. The presence of both type of reads is mandatory to provide the full number of reads covering the junction region. To know which information are provided by the supported tool please check fSet

Usage

supportingReads(list, fusion.reads=c("encompassing","spanning"), parallel=FALSE)

Arguments

list

a list of fSet objects

fusion.reads

it allows to extract spanning reads associated to the SeedCount slot or encompassing reads associated to the RescuedCount

parallel

option to run a parallel version of the function, default FALSE

Examples

tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19")
supporting.reads <- supportingReads(tmp, fusion.reads="spanning")
supporting.reads