oncofuseRun {chimera} | R Documentation

## 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.

### Author(s)

Raffaele A Calogero

### Examples

    #tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19")
    #installOncofuse()
    #of.out <- oncofuseRun(tmp, tissue="EPI")

[Package chimera version 1.24.0 Index]