KEGGAnalysis: KEGGAnalysis

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

Description

Function to make KEGG analysis.

Usage

KEGGAnalysis(fitMain, whichContrasts, comparison.Name, outputDir,
  anotPackage, organisme, my.IDs, addGeneNames = TRUE, fileOfLinks,
  cutoffMethod = c("adjusted", "unadjusted"),
  P.Value.cutoff = rep(0.05, length(whichContrasts)), pval = 0.05,
  thrLogFC = NULL, minNumGens = 0)

Arguments

fitMain	????
whichContrasts	????
comparison.Name	????
outputDir	????
anotPackage	????
organisme	????
my.IDs	????
addGeneNames	????
fileOfLinks	????
cutoffMethod	????
P.Value.cutoff	????
pval	????
thrLogFC	????
minNumGens	????

Examples

## Not run: 
load("./ResultsDir/fit.Rda")
wCont <- 1:3
comparison.Name <-"Estudi"
outputDir <- "./ResultsDir"
orgPackage <-"org.Hs.eg"
organisme <-"hsa"
load("./ResultsDir/Entrezs.Rda")
addGeneNames <- TRUE
linksFileName <- "Links.txt"
cutoffMethod <-"unadjusted"
pval <- 0.05
minNumGens <-0
runMulticore <- 0

KEGGResult <- BasicP::KEGGAnalysis(fitMain = fit.main, whichContrasts = wCont,
comparison.Name = comparison.Name, outputDir = outputDir, anotPackage = orgPackage,
organisme = organisme, my.IDs = entrezTable, addGeneNames = addGeneNames,
fileOfLinks = linksFileName, cutoffMethod = cutoffMethod,
P.Value.cutoff = rep(0.05, length(wCont)), pval = pval,thrLogFC = 1,
minNumGens = minNumGens)

## End(Not run)

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