runCPH: runCPH: runs cox proportional hazard models against patients...

Description Usage Arguments Details Value

View source: R/runCPH.R

Description

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.

Usage

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runCPH(exprRange = 0.33, percExpr = 0.8, sep = ";", exprSep = sep,
  outputDir = getwd(), silent = F, survData = NULL,
  expressionData = NULL, simple = T, analysisName = paste("run",
  gsub("([ ]|[:])", "_", format(Sys.time()))), scan = T,
  geneList = NULL)

Arguments

exprRange

top and bottom quantiles of expression values to select samples for testing

percExpr

filter for minimum percentage of samples required to be expression a gene to select genes for testing

sep

default separator for delimited survival and sample id files supplied

exprSep

default separator for expression file supplied

outputDir

location to write output files

silent

boolean return the full set of statistics as a data frame

analysisName

stub to add to output file names

sampleDataFile

name of the a delimited sample data file, first column should contain the sample id's for samples to match in survival and expression data

survivalDataFile

name of the delimited survival data file, first column should contain the sample ids to match with sample data and expression data. If this file is not specified uses default data created for TCGA SKCM samples

expressionDataFile

name of the delimited expression data file, second row should contain the sample ids as column headings to match with sample data and expression data. If this file is not specified uses default data created for TCGA SKCM samples normalised expression values. NB when this file is read in the first line will be skipped.

Details

It will also perform a limma differential gene expression test for the significance of the fold change between the top and bottom n percent of expression values

Value

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


PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.