oncofuseRun {chimera} | R Documentation |
A list of fSet objects can be annotated using the Oncofuse java application.
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
#tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19") #installOncofuse() #of.out <- oncofuseRun(tmp, tissue="EPI")