getTopGeneSets {HTSanalyzeR} | R Documentation |
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)
getTopGeneSets(object, ...)
object |
an object. When this function is implemented as the S4 method of class |
... |
other arguments (see below for the arguments supported by the method of
class |
a single character value: 'HyperGeo.results' or 'GSEA.results'
a character vector specifying the names of gene set collections from which the top significant gene sets will be selected
a single integer or numeric value specifying to select how many gene sets of top significance.
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.
a list of character vectors, each of which contains the names of top significant gene sets for each gene set collection
Xin Wang xw264@cam.ac.uk
## 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)