multipleComp: multipleComp

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

Description

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

whichContrasts	Vector that determie the contrast to do.
comparisonName	Name of the comparisons.
outputDir	Path of the file created.
anotPackage	Annotation package.
linksFile	Name of the LinksFile.
multCompMethod	Method to make the comparation.
adjustMethod	Method to apply in the adjust.
P.Value.cutoff	Cutoff value for p.value.

Examples

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

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