survAnal: survAnal: runs cox proportional hazard models against...

Description Usage Arguments Value

View source: R/survAnal.R

Description

derived from 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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survAnal(survData = NULL, exprData = NULL, geneData = NULL,
  survTime = "time", exprRange = 0.33, survStatus = "status",
  mcores = 4, summarise = TRUE)

Arguments

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

exprRange

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

survStatus

name of suvival censoring column

mcores

number of cores for bioparallel

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.