clusterAnalysis: clusterAnalysis

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

Function to make the cluster analysis.

Usage

clusterAnalysis(expres, genes, samples, sampleNames, comparisonName,
  anotPackage, my.symbols = NULL, outputDir, fileOfLinks, numClusters,
  rowDistance, colDistance, RowVals = TRUE, ColVals = TRUE, colorsSet,
  colsForGroups, escala, densityInfo = "none", cexForColumns, cexForRows,
  plotProfiles = FALSE, Title = "", csvType = NULL)

Arguments

expres	Expresion oused to perform the clusters.
genes	????
samples	????
sampleNames	Name of the samples of the study.
comparisonName	Name of the comparison. To identify the output
anotPackage	Annotation package.
my.symbols	????
outputDir	Path of the file created.
fileOfLinks	Name of the links file.
numClusters	????
rowDistance	Row distance in the clusters.
colDistance	Column distance in the clusters.
RowVals	????
ColVals	?????
colorsSet	???
colsForGroups	Colors of each group for the plots.
escala	???
densityInfo	???
cexForColumns	Cex for the columns.
cexForRows	Cex for the rows.
plotProfiles	???
Title	Title of the plot.
csvType	Csv type of the output.

Examples

 ## Not run: 
for(i in 1:length(compName)) {
 matrices <- as.logical(apply(abs(as.matrix(cont.matrix[, wCont[[i]]])), 1, sum))
 s2clust <-  which(as.logical(apply(design[, matrices], 1, sum)))
 pvalType <- ifelse(adjMethod[i] == "none", "pvalues", "adj-pvalues")
 geneListFName <- paste("geneList", compName[i], pvalType, "LT", pValCutOff[i], "Rda", sep = ".")
 pal <- colorpanel(n = 32, low = "green", mid = "white", high = "magenta")
 load("./ResultsDir/geneList.Group1.pvalues.LT.0.01.Rda")
 clust <- BasicP::clusterAnalysis(expres = exprs.filtered,
                                  genes = geneList,
                                  samples = s2clust,
                                  sampleNames = as.character(targets$ShortName)[s2clust],
                                  comparisonName = "Compar 1",
                                  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(rep("pink", 5), rep("blue", 5)),
                                  cexForColumns = 0.8,
                                  cexForRows = 0.8,
                                  Title = paste("Compar 1 with", pvalType, "<", pValCutOff[i],
                                                ifelse(minLogFoldChange[i] == 0, "",
                                                       paste0("\n and |logFC|>=",
                                                              minLogFoldChange[i]))),
                                  csvType = "csv2")
}

## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.