getTopGeneSets {HTSanalyzeR} | R Documentation

## Select top significant gene sets from GSEA results

### Description

This is a generic function.

When implemented as the S4 method of class `GSCA`, this function selects top significant gene sets from GSEA results for user-specified gene collections. If 'ntop' is given, then top 'ntop' significant gene sets in gene set collections 'gscs' will be selected and their names will be returned. If 'allSig=TRUE', then all significant (adjusted p-value < 'pValueCutoff' see help("analyze")) gene sets will be selected and their names will be returned.

To use this function for objects of class `GSCA`:

getTopGeneSets(object, resultName, gscs, ntop=NULL, allSig=FALSE)

### Usage

    getTopGeneSets(object, ...)

### Arguments

`object` | an object. When this function is implemented as the S4 method of class `GSCA`, this argument is an object of class `GSCA`.
`...` | other arguments (see below for the arguments supported by the method of class `GSCA`)

resultName:

  a single character value: 'HyperGeo.results' or 'GSEA.results'

gscs:

  a character vector specifying the names of gene set collections from which the top significant gene sets will be selected

ntop:

  a single integer or numeric value specifying to select how many gene sets of top significance.

allSig:

  a single logical value. If 'TRUE', all significant gene sets (GSEA adjusted p-value < 'pValueCutoff' of slot 'para') will be selected; otherwise, only top 'ntop' gene sets will be selected.

### Value

a list of character vectors, each of which contains the names of top significant gene sets for each gene set collection

### Author(s)

Xin Wang xw264@cam.ac.uk

### Examples

    ## Not run:
    library(org.Dm.eg.db)
    library(KEGG.db)
    ##load data for enrichment analyses
    data("KcViab_Data4Enrich")
    ##select hits
    hits <- names(KcViab_Data4Enrich)[which(abs(KcViab_Data4Enrich) > 2)]
    ##set up a list of gene set collections
    PW_KEGG <- KeggGeneSets(species = "Dm")
    gscList <- list(PW_KEGG = PW_KEGG)
    ##create an object of class 'GSCA'
    gsca <- new("GSCA", listOfGeneSetCollections=gscList, geneList =
    KcViab_Data4Enrich, hits = hits)
    ##print summary of gsca
    summarize(gsca)
    ##do preprocessing (KcViab_Data4Enrich has already been preprocessed)
    gsca <- preprocess(gsca, species="Dm", initialIDs = "Entrez.gene",
    keepMultipleMappings = TRUE, duplicateRemoverMethod = "max",
    orderAbsValue = FALSE)
    ##print summary of gsca again
    summarize(gsca)
    ##do hypergeometric tests and GSEA
    gsca <- analyze(gsca, para = list(pValueCutoff = 0.05, pAdjustMethod
    = "BH", nPermutations = 1000, minGeneSetSize = 100,exponent = 1))
    ##print summary of results
    summarize(gsca, what="Result")
    ##print top significant gene sets in GO.BP
    topPWKEGG<-getTopGeneSets(gsca, "GSEA.results", "PW_KEGG", allSig=TRUE)

    ## End(Not run)

[Package HTSanalyzeR version 2.38.0 Index]