survFit: survAnal: runs cox proportional hazard models against...
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

Description Usage Arguments Value Examples

The runCPH function will process three separate file one with sample ids one with survival data and one with expression values. In test mode if a list of sample ids are supplied but not the other two files it assumes the ids are from the TCGA SKCM data set and uses a cached version of the normalised expression values from the TCGA SKCM data set and a currated set of survival data.

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survFit(survData = NULL, exprData = NULL, geneData = NULL,
  survTime = "time", survStatus = "status", mcores = 4,
  verbose = F)

`survData`	survival data must contain a time and status
`exprData`	normalised gene expression data
`geneData`	names of the genes to be tested (must be in the rownames of exprData)
`survTime`	name of survival time column
`survStatus`	name of suvival censoring column
`mcores`	number of cores for bioparallel
`exprRange`	top and bottom quantiles of expression values to select samples for testing

the function creates several csv output files with the Cox PH results, the Limma DGE results, a combined set of both results and a set of those genes for which the DGE result is significant at 0.05 FDR

analysisName="test3"
exprSep=","
res <- runCPH(sampleDataFile=sampleDataFile,expressionDataFile=expressionDataFile,
              survivalDataFile=survivalDataFile,
              analysisName=analysisName,exprSep=exprSep)