writeReportHTSA {HTSanalyzeR} | R Documentation

## Write HTML reports for enrichment and/or network analyses

### 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)

[Package HTSanalyzeR version 2.38.0 Index]