GOAnalysis: GOAnalysis

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

Description

Function that do GOAnalysis

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

comparison.Name	Name of the comparison. To identify the output.
outputDir	Path of the file created.
anotPackage	Annotation package.
addGeneNames	Vector of the gene names.
fileOfLinks	Name of the links file.
thrLogFC	Threshold for the logarithm Fold Change
P.Value.cutoff	Maximum value for the p.value.
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)

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