survAnal2: survAnal: runs cox proportional hazard models against...
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

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.

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survAnal2(survData = NULL, exprData = NULL, survTime = "time",
  exprRange = 0.33, survStatus = "status", mcores = 4,
  summarise = TRUE, geneList = NULL)

`survData`	survival data must contain a time and status
`exprData`	normalised gene expression data
`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
`geneData`	names of the genes to be tested (must be in the rownames of exprData)

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 May 6, 2019, 6:45 p.m.