getSurvival: Perform survival analysis based on gene expression data

In RTCGAToolbox: A new tool for exporting TCGA Firehose 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(accmini)
clinicData <- getData(accmini,"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=accmini,geneSymbols=c("FCGBP"),sampleTimeCensor=survData)

Example output

NULL
Warning message:
This function is no longer maintained and will be retired. 

RTCGAToolbox documentation built on Nov. 8, 2020, 5:34 p.m.