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

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 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)

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 top 'ntop' most significant p-values.

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. (see function 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 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'.

Author(s)

Xin Wang, Camille Terfve

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)

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