getTopGeneSets: Select top significant gene sets from GSEA results

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

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 [e-mail]

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)

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.