report: Write HTML reports for enrichment or network analyses

Description

This is a generic function.

When implemented as the method of class GSCA or NWA, this function produces reports for either the Gene Set Collection Analysis or the Network Analysis.

To use report for objects of class GSCA or NWA:

report(object, experimentName="Unknown", species=NULL, ntop=NULL, allSig=FALSE, keggGSCs=NULL, goGSCs=NULL, reportDir="HTSanalyzerReport")

Usage

report(object, ...)

Arguments

object

an object. When implemented as S4 methods of class GSCA or NWA, this argument is either an object of class GSCA or NWA.

...

other arguments. (see below for the arguments supported by the method of class GSCA or NWA)

Details

This function take in the objects of the two wrapper classes (GSCA and NWA) and writes a report into the user-specified directory. An index HTML file containing a summary of all results and hyperlinked tabs to more detailed results will be generated in the root directory. The other HTML files will be stored in a subdirectory called 'html'. All images including GSEA plots, enrichment maps and the subnetwork figure will be produced in a subdirectory called 'image'. All documents or text files such as the files containing significant gene sets of the hyper- geometric test results will be stored in a subdirectory called 'doc'.

Examples

Run this code

## Not run: 
# ##(see the vignette for details about the preprocessing of this data set)
# library(KEGG.db)
# library(GO.db)
# library(AnnotationDbi)
# ##report for a GSCA object
# data("KcViab_GSCA")
# ##append gene set terms to results
# KcViab_GSCA<-appendGSTerms(KcViab_GSCA, keggGSCs="PW_KEGG", 
# goGSCs=c("GO_BP","GO_MF","GO_CC"))
# report(object=KcViab_GSCA, experimentName="KcViab", species="Dm",
# allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC"),
# reportDir="HTSanalyzerGSCAReport")
# browseURL(file.path(getwd(), "HTSanalyzerGSCAReport", "index.html"))
# ##report for a NWA object
# data("KcViab_NWA")	
# report(object=KcViab_NWA, experimentName="KcViab", species="Dm",
# allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC"),
# reportDir="HTSanalyzerNWReport")
# browseURL(file.path(getwd(), "HTSanalyzerNWReport", "index.html"))
# ## End(Not run)

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