getReport {RTCGAToolbox} | R Documentation |
getReport
draws a circle plot into your workin director to show log fold changes for differentially expressed genes, copy number alterations and mutations.
getReport(dataObject, DGEResult1 = NULL, DGEResult2 = NULL, geneLocations)
dataObject |
This must be |
DGEResult1 |
Differential gene expression results object (Optional) |
DGEResult2 |
Differential gene expression results object (Optional) |
geneLocations |
Gene coordinates. |
Draws a circle plot
data(accmini) require("Homo.sapiens") locations <- genes(Homo.sapiens,columns="SYMBOL") locations <- as.data.frame(locations) locations <- locations[,c(6,1,5,2:3)] locations <- locations[!is.na(locations[,1]),] locations <- locations[!duplicated(locations[,1]),] rownames(locations) <- locations[,1] ## Not run: getReport(dataObject=accmini,DGEResult1=t1[[1]],geneLocations=locations) ## End(Not run)