TCGAvisualize_SurvivalCoxNET need to be modified

fireindark707 commented 7 years ago

Hello, Thanks to TCGAbiolinks group for your work. But TCGAvisualize_SurvivalCoxNET cannot work well at present.

I tried this code from help documents.

require(dnet) # to change org.Hs.string <- dRDataLoader(RData = "org.Hs.string")

TabCoxNet <- TCGAvisualize_SurvivalCoxNET(dataClin, dataFilt, Genelist = rownames(dataSurv), scoreConfidence = 700, org.Hs.string = org.Hs.string, titlePlot = "Case Study n.1 dnet")

But it can't run, there are many warnings and errors in the code of TCGAvisualize_SurvivalCoxNET function. The update and Revision of format of GDC clinic data may be the reason.

For example, the following code from visualize.R is not right. "days_to_last_followup" should be "days_to_last_follow_up","age_at_initial_pathologic_diagnosis" should be a "age_at_diagnosis".

cfu <- as.data.frame(subset(cfu, select=c("bcr_patient_barcode", "days_to_last_followup", "days_to_death", "vital_status", "age_at_initial_pathologic_diagnosis", "gender")

And, like this. "Dead" should be "dead".

cfu[which(cfu$status=="Dead"),"time"]<- cfu[which(cfu$status=="Dead"),"timeDead"] cfu[which(cfu$status=="Dead"),"status"]<-1

I'am trying to repair this function, but I think this is an important issue, maybe other functions are also affected by this problem. So I decide to submit this issue.

Rangers107 commented 5 years ago

how to solve it?

Rangers107 commented 5 years ago

I have the same problem

BioinformaticsFMRP / TCGAbiolinks