analyzeGeneSetCollections {HTSanalyzeR} | R Documentation

## 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)

### Details

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

### 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.

### Author(s)

John C. Rose, Xin Wang

### See Also

`analyze`

### Examples

    ## 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)

[Package HTSanalyzeR version 2.38.0 Index]