writeReportHTSA: Write HTML reports for enrichment and/or network analyses

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This function writes an HTML report following a complete analysis of a data set with the objects of class GSCA and/or NWA.

Usage

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

Arguments

gsca	an object of class GSCA
nwa	an object of class NWA
experimentName	a single character value specifying the name of the experiment (just for you own record)
species	a single character value specifying the species for which the data should be read. The current version supports one of the following species: "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_ norvegicus"), "Mm" ("Mus_musculus"), "Ce" ("Caenorhabditis_elegans").
ntop	a single integer value specifying the number of plots to be produced for the GSEA analysis. For each gene set collection, plots are produced for the 'ntop' most significant gene sets.
allSig	a single logical value determining whether or not to generate plots for all significant gene sets. A gene set is significant if its corresponding adjusted p-value is less than the pValueCutoff set in function analyze.
keggGSCs	a character vector of the names of all KEGG gene set collections. This will help create web links for KEGG terms.
goGSCs	a character vector of the names of all GO gene set collections. This will help create web links for GO terms.
reportDir	a single character value specifying the directory to store reports

Details

This function takes in the objects of the two wrapper classes (GSCA and NWA) and writes a report into a user-specified directory. An index HTML file containing a summary of all results and hyperlinked tabs linking 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 the GSEA plots, enrichment maps and 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 hypergeometric test results will be stored in a subdirectory called 'doc'.

Author(s)

Xin Wang, Camille Terfve

See Also

report, reportAll

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
writeReportHTSA(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)

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