chimera (version 1.8.5)

oncofuseRun: A function to annotate fusions with Oncofuse. Oncofuse is a naive bayesian classifier. Its goal is to identify those fusion sequences with higher probability of being driver than passenger events

Description

A list of fSet objects can be annotated using the Oncofuse java application.

Usage

oncofuseRun(listfSet, tissue=c("EPI","HEM","MES","AVG"), plot=FALSE)

Arguments

listfSet

A list of fSets

tissue

Type of tissue in which the fusion was detected. EPI epithelial, HEM ematological, MES mesenchimal, AVG average expression

plot

plotting the expression gain score versus the passenger mutation probability. For mor einfo please see Shugay et al. Bioinformatics 2013:29,2539

Value

The output is a dataframe containing the output of Oncofuse. For more info on Oncofuse please see Shugay et al. Bioinformatics 2013, 29, 2539.

Examples

#tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hs")
#installOncofuse()
#of.out <- oncofuseRun(tmp, tissue="EPI")