doMultCompAnalysis: doMultCompAnalysis

In Merguerrero/BasicP: Function to support a microarray data analysis pipeline

Description

Function for make the comparative analysis.

Usage

doMultCompAnalysis(mcPar)

Arguments

mcPar

List object that contains the parameters.

Examples

## Not run: 
mcParsList <- list()
compName <- c("Group1", "Group2")
wCont <- 1:ncol(cont.matrix)
pValCutOff <- c(0.01, 0.01) 
adjMethod <- c("none", "none")
minLogFoldChange <- c(1, 1) 
for(i in 1:length(compName))
{  
  mci <- list(fitMain = fitMain,
              fitFileName = fitFileName,
              whichContrasts = wCont[[i]],
              comparisonName = compName[i],
              titleText = paste("for",ifelse(adjMethod[i]=="none",
                                             "p-values","adj. p-values"), "<", pValCutOff[i], "and |logFC| >",
                                minLogFoldChange[i], sep = " "),
              anotPackage = "org.Hs.eg",
              my.symbols = symbolsTable,
              outputDir = outputDir,
              fileOfLinks = linksFile,
              multCompMethod = "separate",
              adjustMethod = adjMethod[i], 
              selectionType = "any",
              P.Value.cutoff = pValCutOff[i],
              plotVenn = TRUE,
              colsVenn = NULL,
              vennColors= c("red","yellow","green","blue","pink"),  
              cexVenn = 1,
              geneListFName = paste("geneList",compName[i],
                                    ifelse(adjMethod[i]=="none","pvalues","adj-pvalues"),
                                    "LT",pValCutOff[i],"Rda",sep = "."),
              minLogFC = minLogFoldChange[i],
              csvType = csvType)
  
  mcParsList <- add2parsList(mcParsList, mci)
}

for(ix in 1:length(mcParsList))
{
  geneList.MCi <- BasicP::doMultCompAnalysis(mcParsList[ix])   
}

## End(Not run)

Merguerrero/BasicP documentation built on May 20, 2019, 2:24 p.m.