HTSanalyzeR (version 2.24.0)

summarize: Print summary information for an object of class GSCA or NWA

Description

This is a generic function.

When implemented as the S4 method for objects of class GSCA or NWA, this function prints a summary of information about the slots of these classes.

To use this function for objects of class GSCA or NWA:

summarize(object, what="ALL")

Usage

summarize(object, ...)

Arguments

object

an object. When this function is implemented as the S4 method of class GSCA or NWA, this argument is an object of class GSCA or NWA.

...

other arguments depending on class (see below for the arguments supported by the method of class GSCA and NWA)

Details

For an object of class GSCA, the key words are 'GSC' (the slot 'listOfGeneSetCollections'), 'GeneList' (the slot 'geneList'), 'Hits' (the slot 'hits'), 'Para' (the slot 'para'), 'Result' (the slot 'result') and 'ALL' (all slots).

For an object of class NWA, the key words include 'Pval' (the slot 'pvalue'), 'Phenotype' (the slot 'phenotype'), 'Interactome' (the slot 'interactome'), 'Para' (the slot 'fdr'), 'Result' (the slot 'result') and 'ALL' (all slots).

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")
# ## End(Not run)