doClusterAnalysis: doClusterAnalysis

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

Description

Function to perform cluster analysis

Usage

doClusterAnalysis(clustPar)

Arguments

clustPar

List object that contains the parameters needed to carry out the analysis.

Examples

## Not run: 
clustParsList <- list()
for(i in 1:length(compName))
{
  clustPar <- list(expres = NULL,
                   expresFileName = "exprs.filtered.Rda",
                   geneListFName = paste("geneList",  compName[i],     ifelse(adjMethod[i]=="none","pvalues","adj-pvalues"), "LT", pValCutOff[i], "Rda", sep = "."),
                   genes2cluster = NULL, 
                   samples2cluster = s2clust, 
                   sampleNames = as.character(targets$ShortName)[s2clust], 
                   comparisonName = compName[i], 
                   anotPackage = "org.Hs.eg",
                   my.symbols = symbolsTable,
                   outputDir = outputDir,
                   fileOfLinks = linksFile,
                   numClusters = 2,
                   rowDistance = NULL,
                   colDistance = NULL,
                   RowVals = TRUE,
                   ColVals = FALSE,
                   escala = "row",
                   colorsSet = pal,
                   densityInfo = "density",
                   colsForGroups = c("pink","pink","pink","pink","pink","blue","blue","blue","blue","blue"),
                   cexForColumns = 0.8,
                   cexForRows = 0.8,
                   Title = paste(compName[i],
                                 "with",
                                 ifelse(adjMethod[i]=="none","pvalues","adj-pvalues"),
                                 "<",
                                 pValCutOff[i], ifelse(minLogFoldChange[i]==0, "", paste("\n and |logFC|>=", minLogFoldChange[i], sep=""))),
                   paste("Comparison:", compName[i], sep=" "),
                   csvType = csvType)
  
  clustParsList <- add2parsList(clustParsList, clustPar)
}

for(ix in 1:length(clustParsList))
{
 hm.Estudi <- BasicP::doClusterAnalysis(clustParsList[ix])
}

## End(Not run)

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