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

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 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)

what:

a single character value or a character vector of key words specifying what to print (see details below).

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).

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")

## End(Not run)

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