summarize {HTSanalyzeR} | R Documentation

## 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`)

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 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")

    ## End(Not run)

[Package HTSanalyzeR version 2.38.0 Index]