analyzeGeneSetCollections: Hypergeometric tests and Gene Set Enrichment Analyses over a list of gene set collections

Description

This function takes a list of gene set collections, a named phenotype vector (with names of the phenotype vector as the universe), a vector of hits (gene names only) and returns the results of hypergeometric and gene set enrichment analyses for all of the gene set collections (with multiple hypothesis testing corrections).

Usage

analyzeGeneSetCollections(listOfGeneSetCollections, geneList, hits, 
pAdjustMethod="BH", pValueCutoff=0.05, nPermutations=1000, 
minGeneSetSize=15, exponent=1, verbose=TRUE, doGSOA=TRUE, doGSEA=TRUE)

Arguments

listOfGeneSetCollections

a list of gene set collections (a 'gene set collection' is a list of gene sets). Even if only one collection is being tested, it must be entered as an element of a 1-element list, e.g. ListOfGeneSetCollections = list(YourOneGeneSetCollection). Naming the elements of listOfGeneSetCollections will result in these names being associated with the relevant data frames in the output (meaningful names are advised)

geneList

a numeric or integer vector of phenotypes in descending or ascending order with elements named by their EntrezIds (no duplicates nor NA values)

hits

a character vector of the EntrezIds of hits, as determined by the user

pAdjustMethod

a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details)

pValueCutoff

a single numeric value specifying the cutoff for p-values considered significant

nPermutations

a single integer or numeric value specifying the number of permutations for deriving p-values in GSEA

minGeneSetSize

a single integer or numeric value specifying the minimum number of elements in a gene set that must map to elements of the gene universe. Gene sets with fewer than this number are removed from both hypergeometric analysis and GSEA.

exponent

a single integer or numeric value used in weighting phenotypes in GSEA (see the function gseaScores)

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

doGSOA

a single logical value specifying to perform gene set overrepresentation analysis (when doGSOA=TRUE) or not (when doGSOA=FALSE)

doGSEA

a single logical value specifying to perform gene set enrichment analysis (when doGSEA=TRUE) or not (when doGSEA=FALSE)

Value

HyperGeo.results: a list of data frames containing the results for all gene set collections in the input.
GSEA.results: a similar list of data frames containing the results from GSEA. As an example, to access the GSEA results for a gene set collection named "MyGeneSetCollection", one would enter: output$GSEA.results$MyGeneSetCollection
Sig.pvals.in.both: a list of data frames containing the gene sets with p-values considered significant in both hypergeometric test and GSEA, before p-value correction. Each element of the list contains the results for one gene set collection.
Sig.adj.pvals.in.both: a list of data frames containing the gene sets with p-values considered significant in both hypergeometric test and GSEA, after p-value correction. Each element of the list contains the results for one gene set collection.

Details

All gene names must be EntrezIds in 'listOfGeneSetCollections', 'geneList', and 'hits'.

Examples

Run this code

## Not run: 
# library(org.Dm.eg.db)
# library(GO.db)
# library(KEGG.db)
# ##load phenotype vector (see the vignette for details about the 
# ##preprocessing of this data set)
# data("KcViab_Data4Enrich")
# ##Create a list of gene set collections for Drosophila melanogaster (Dm)
# GO_MF <- GOGeneSets(species="Dm", ontologies="MF")
# PW_KEGG <- KeggGeneSets(species="Dm")
# ListGSC <- list(GO_MF=GO_MF, PW_KEGG=PW_KEGG)
# ##Conduct enrichment analyses
# GSCAResults <- analyzeGeneSetCollections(
# 		listOfGeneSetCollections=ListGSC,
# 		geneList=KcViab_Data4Enrich,
# 		hits=names(KcViab_Data4Enrich)[which(abs(KcViab_Data4Enrich)>2)],
# 		pAdjustMethod="BH",
# 		nPermutations=1000,
# 		minGeneSetSize=200,
# 		exponent=1,
# 		verbose=TRUE
# )
# ## End(Not run)