chimera (version 1.14.0)

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"), org=c("hg19","hg38"), threads=1, plot=FALSE, type=c("listfSet","coordDf"))

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

org

Supported genome assembly version. IMPORTANT: the genome version used for the fusion detection and for the oncofuse analysis need to be same

threads

number of threads that Oncofuse will use

plot

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

type

listfSet a list of fSet objects or coordDf a dataframe of coordinates of fusions in the format required by Oncofuse

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="hg19")
#installOncofuse()
#of.out <- oncofuseRun(tmp, tissue="EPI")