report: Write HTML reports for enrichment or network analyses

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

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)

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 results. For each gene set collection, plots are produced for the 'ntop' most significant gene sets.

allSig:

a single logical value indicating 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 the function analyze. (see help(analyze) for more details)

keggGSCs:

a character vector of names of all KEGG gene set collections. This will help create web links for KEGG terms.

goGSCs:

a character vector of 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 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'.

Author(s)

Xin Wang, Camille Terfve

See Also

reportAll, writeReportHTSA

Examples

## 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)

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