oncofuseRun: A function to annotate fusions with Oncofuse. Oncofuse is a...
In chimera: A package for secondary analysis of fusion products

Description Usage Arguments Value Author(s) Examples

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

1	oncofuseRun(listfSet, tissue=c("EPI","HEM","MES","AVG"), org=c("hg19","hg38"), threads=1, plot=FALSE, type=c("listfSet","coordDf"))

`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

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

Raffaele A Calogero

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

chimera documentation built on Nov. 8, 2020, 5:16 p.m.