multipleComp: multipleComp Function to make multiple comparations.

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

Description

multipleComp Function to make multiple comparations.

Usage

multipleComp(fitMain, whichContrasts, comparisonName, titleText, outputDir,
  anotPackage, my.symbols = NULL, linksFile,
  multCompMethod = "separate", adjustMethod = "none",
  selectionType = c("any", "all", "anyDown", "anyUp", "allDown",
  "allUp"), P.Value.cutoff = 0.05, plotVenn, colsVenn = NULL,
  vennColors, cexVenn = 1, geneListFName = paste("geneList",
  comparisonName, "Rda", sep = "."), csvType = NULL, minLFC = 0)

Arguments

fitMain	Object resulting from lmFit estimation
whichContrasts	Vector that determie the contrast to do.
comparisonName	Name of the comparisons.
titleText	Main title for the multiple comparison analysis
outputDir	Path of the file created.
anotPackage	Annotation package.
my.symbols	List of gene symbols to be used to annotate he output.
linksFile	Name of the LinksFile.
multCompMethod	Method to make the comparation.
adjustMethod	Method to apply in the adjust.
selectionType	Selection method to be used.
P.Value.cutoff	Cutoff value for p.value.
plotVenn	Boolean variable to decide if plot diagram has to be used.
colsVenn	Columnns for the Venn diagram
vennColors	Columns for the Venn diagram
cexVenn	Expansion coefficient for Venn diagram labels
geneListFName	Name of file containg gene list.
csvType	Type of csv file to be written.
minLFC	minimum log Fold change for selecting genes.

Examples

## Not run: 
compName <- c("Group1")
wCont <- 1:3
pValCutOff <- c(0.01)
adjMethod <- c("none")
minLogFoldChange <- c(1)
load("./ResultsDir/Symbols.Rda")
pvalType <- ifelse(adjMethod == "none", "p-values", "adj. p-values")
titleText <- paste("for", pvalType, "<", pValCutOff, "and |logFC| >", minLogFoldChange)
geneListFName <- paste("geneList", compName, pvalType ,"LT", pValCutOff, "Rda", sep = ".")

geneList <- BasicP::multipleComp(fitMain = fitMain, whichContrasts = wCont,
                                 comparisonName = compName, titleText = titleText,
                                 outputDir = outputDir, anotPackage = "org.Hs.eg",
                                 my.symbols = symbolsTable, linksFile = linksFile,
                                 multCompMethod = "separate",
                                 adjustMethod = adjMethod, selectionType = "any",
                                 P.Value.cutoff = pValCutOff, plotVenn = TRUE, colsVenn = NULL,
                                 vennColors = c("red", "yellow", "green", "blue", "pink"),
                                 cexVenn = 1, geneListFName = geneListFName, csvType = csvType,
                                 minLFC = minLogFoldChange)

## End(Not run)

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