report {HTSanalyzeR} | R Documentation

## Write HTML reports for enrichment or network analyses

### 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)

[Package HTSanalyzeR version 2.38.0 Index]