HTSanalyzeR (version 2.24.0)

reportAll: Write HTML reports for both the enrichment and network analyses

Description

This is a generic function.

When implemented as the method of class GSCA and NWA, this function produces a report for both the results of Gene Set Collection Analysis and the Network Analysis.

To use reportAll for objects of class GSCA and NWA:

reportAll(gsca, nwa, experimentName="Unknown", species=NULL, ntop=NULL, allSig=FALSE, keggGSCs=NULL, goGSCs=NULL, reportDir="HTSanalyzerReport")

Usage

reportAll(gsca, nwa, ...)

Arguments

gsca

an object of class GSCA (see help(GSCA))

nwa

an object of class NWA (see help(NWA))

...

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

Details

This function takes 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 and subnetwork figure will be produced in a sub- directory called 'image'. All documents or text files such as the files containing significant gene sets of the hypergeometric test results will be stored in a subdirectory called 'doc'.

See Also

report, writeReportHTSA

Examples

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