reportAll {HTSanalyzeR} | R Documentation

## Write HTML reports for both the enrichment and network analyses

### 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)

[Package HTSanalyzeR version 2.34.1 Index]