RTCGA (version 1.2.2)

getSurvival: Perform survival analysis based on gene expression data

Description

getSurvival draws a KM plot and show survival analysis results between groups that are defined by gene expression data

Usage

getSurvival(dataObject, numberofGroups = 2, geneSymbols, sampleTimeCensor)

Arguments

dataObject

This must be FirehoseData object.

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.

Value

• Draws a KM plot

Examples

## 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)