GOoverrepresentation: GOoverrepresentation

In MarianoRuzJurado/RNASeq: A workflow for RNA-Seq analysis.

Description

runs a GO over-representation test

Usage

GOoverrepresentation(collectResults,
                      OrgDb,
                      pvalueCutoff,
                      pAdjustMethod,
                      qvalueCutoff,
                      minGSSize,
                      maxGSSize)

Arguments

collectResults	= a list, with sub lists
OrgDb	= organism db (e.g org.Hs.eg.db)
pvalueCutoff	= Cutoff value of pvalue
pAdjustMethod	= one method of the following: "holm", "hochberg", "hommel","bonferroni","BH","BY","fdr","none"
qvalueCutoff	= Cutoff value of qvalue
minGSSize	= minimal size of genes annotated by ontology term for testing
maxGSSize	= maximal size of genes annotated for testing

Details

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("clusterProfiler")

Value

.xls files with results for molecular function, biological process and celular component and results are added to your collectResults list

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x)
{
  }

MarianoRuzJurado/RNASeq documentation built on Feb. 5, 2020, 8:46 p.m.