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

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

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.

Usage

## S4 method for signature 'GSCA'
summarize(object, what = "ALL")

## S4 method for signature 'NWA'
summarize(object, what = "ALL")

Arguments

object	A GSCA object or NWA object.
what	A single character value or a character vector of key words specifying what to print (see Methods below). Default will print a summary of all information.

Value

In the end, this function would return a summary of the NWA object.

In the end, this function would return a summary of the NWA object.

Methods (by class)

• GSCA: 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).

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

Examples

# =================================================================
# GSCA class
## load a GSCA object(see the examples of analyze GSCA for details)
data(d7_gsca)

## summarize d7_gsca
summarize(d7_gsca, what = "ALL")
summarize(d7_gsca, what = "Result")
## Not run: 
# =================================================================
# NWA class
## load a NWA object(see the examples of analyze NWA for details)
data(d7_nwa)

## summarize d7_nwa
summarize(d7_nwa, what = "ALL")
summarize(d7_nwa, what = "Result")

## End(Not run)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.