getSurvival {RTCGAToolbox} | R Documentation |
getSurvival
draws a KM plot and show survival analysis results between groups that are defined by gene expression data
getSurvival(dataObject, numberofGroups = 2, geneSymbols, sampleTimeCensor)
dataObject |
This must be |
numberofGroups |
Can be set as 2 or 3. (Default 2) Order and divide samples into n groups by using gene expression data. |
geneSymbols |
Gene symbol that is going to be tested |
sampleTimeCensor |
a data frame that stores clinical data. First column should store sample IDs, second column should have time and third column should have event information. For more information please see vignette. |
Draws a KM plot
## get data with getFirehoseData function and call survival analysis ## Always check clinical data file for structural changes data(RTCGASample) clinicData <- getData(RTCGASample,"clinical") clinicData = clinicData[,3:5] clinicData[is.na(clinicData[,3]),3] = clinicData[is.na(clinicData[,3]),2] survData <- data.frame(Samples=rownames(clinicData),Time=as.numeric(clinicData[,3]), Censor=as.numeric(clinicData[,1])) getSurvival(dataObject=RTCGASample,geneSymbols=c("FCGBP"),sampleTimeCensor=survData)