GOAnalysis: Function that perform enrichment analysis based on the GO for...

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

Description

Function that perform enrichment analysis based on the GO for one gene list and all ontologies with the GOstats package.

Usage

GOAnalysis(fitMain, whichContrasts, comparison.Name, outputDir,
  anotPackage, my.IDs, addGeneNames = TRUE, fileOfLinks,
  thrLogFC = NULL, cutoffMethod = c("adjusted", "unadjusted"),
  P.Value.cutoff = rep(0.05, length(whichContrasts)), pval = 0.05,
  min.count = 3, ontologias = c("MF", "BP", "CC"),
  testDirections = c("over", "under"), minNumGens = 0)

Arguments

fitMain	Object generated by the lmFit function.
whichContrasts	Describes the lmFit contrasts whose associated ids will be analyzed.
comparison.Name	Name of the comparison. To identify the output.
outputDir	Path of the file created.
anotPackage	Annotation package.
my.IDs	Gene identifiers to be analyze. If NULL all provided by the lmFit object will be analyzed.
addGeneNames	Vector of the gene names.
fileOfLinks	Name of the links file.
thrLogFC	Threshold for the logarithm Fold Change
cutoffMethod	Method used to select the genes to be analyzed.
P.Value.cutoff	Maximum value for the p.value.
pval	Pvalue for the enrichment analysis test.
min.count	Minimum number of categories for a result to be considered.
ontologias	Ontologies to be used in the analysis.
testDirections	To decide if the analysis has to be applied to genes upregulated, downregulated or both.
minNumGens	Mimimum number of genes.

Examples

## Not run: 
library(GOstats)
GOResult<-BasicP::GOAnalysis(fitMain = fitMain, whichContrasts = wCont,
comparison.Name = "Estudi", outputDir = outputDir, anotPackage = "org.Hs.eg",
my.IDs = entrezTable, addGeneNames = TRUE, fileOfLinks = linksFile, thrLogFC = 1,
cutoffMethod = "adjusted", P.Value.cutoff = rep(0.05, length(wCont)), pval = 0.01,
min.count = 3, ontologias = c("MF", "BP", "CC"), testDirections = c("over", "under"),
minNumGens = 0)

## End(Not run)

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