DAVIDGODag-class {RDAVIDWebService} | R Documentation

## class "DAVIDGODag

### Description

This concrete class represents an induced GO DAG generated by the DAVID Functional Annotation Chart report a.k.a a DAVIDFunctionalAnnotationChart object.

### Type

This class is a "`Concrete`" one.

### Extends

- GOHyperGResult directly, in order to reuse GOstats functionalities.

### Slots

the ones inherited from GOHyperGResult

### Methods

`show`

  `signature(object="DAVIDGODag")`: basic console output.

`summary`

  `signature(object="DAVIDGODag", ...)`: basic summary console output.

`initialize`

  `signature(object="DAVIDGODag", fileName="character")`: basic cluster report file parser.

`DAVIDGODag`

  `signature(object="DAVIDGODag", fileName="character")`: high level constructor to parse the file report.

`universeMappedCount, universeCounts, counts`

  `signature( object="DAVIDGODag")`: modifications to the corresponding GOstats/Category library functions, to keep the same behavior, for DAVIDGODag object.

`fdrs, benjaminis, bonferronis`

  `signature( object="DAVIDGODag")`: Adjusted method specific p-values for the corresponding nodes/terms.

`terms`

  `signature(object="DAVIDGODag")`: character vector with GO node names.

`popTotals, popHits, listTotals`

  `signature( object="DAVIDGODag")`: integer vector with the number of ids, to use in the EASE score calculations, when building the 2x2 contingency table.

`percentages`

  `signature(object="DAVIDGODag")`: numeric vector with the percentage of the gene list ids present in the term.

`foldEnrichments`

  `signature(object="DAVIDGODag")`:numeric vector with the ratio of the two proportions for each node/term. For example, if 40/400 (i.e. 10%) of your input genes involved in "kinase activity" and the background information is 300/30000 genes (i.e. 1%) associating with "kinase activity", roughly 10%/1%=10 fold enrichment.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

3. Falcon, S; Gentleman, R.; Using GOstats to test gene lists for GO term association, Bioinformatics 23 (2007) 257-258.

### See Also

Other DAVIDGODag: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `benjaminis`, `benjaminis`, `bonferronis`, `bonferronis`, `counts`, `counts`, `fdrs`, `fdrs`, `foldEnrichments`, `foldEnrichments`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `listTotals`, `listTotals`, `percentages`, `percentages`, `popHits`, `popHits`, `popTotals`, `popTotals`, `summary`, `summary`, `summary`, `summary`, `terms`, `terms`, `universeCounts`, `universeMappedCount`, `upsideDown`, `upsideDown`

### Examples

    {
    ##Load the Functional Annotation Chart file report for the input demo
    ##file 2, using data function. Then, create a DAVIDGODag object using
    ##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
    ##obtained from the loaded data.frame funChart2. In addition, we have
    ##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
    ##DAVID/GO.db database are not using the same version.
    data(funChart2)
    davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
    pvalueCutoff=0.001, removeUnattached=TRUE)

    ##Now, we can inspect the enrichment GO DAG using GOstats functionalities:
    ##counts, pvalues, sigCategories, universeCounts, geneMappedCount, etc.
    ##However, oddsRatios, expectedCounts and universeMappedCount are not
    ##available because these results are not available on DAVID's Functional
    ##Annotation Chart report. In addition geneIdUniverse are not the ones of
    ##the universe but the ids on the category (geneIdsByCategory).
    davidGODag
    counts(davidGODag)
    pvalues(davidGODag)
    sigCategories(davidGODag, p=0.0001)
    universeCounts(davidGODag)
    geneMappedCount(davidGODag)
    geneIdsByCategory(davidGODag)
    summary(davidGODag)

    ##In addition, the new nodeData attributes (term, listTotal, popHit,
    ##popTotal, foldEnrichment, bonferroni, benjamini, fdr) can be retrieved.
    terms(davidGODag)
    listTotals(davidGODag)
    popHits(davidGODag)
    popTotals(davidGODag)
    foldEnrichments(davidGODag)
    bonferronis(davidGODag)
    benjaminis(davidGODag)
    fdrs(davidGODag)

    ##The user can even plot the enrichment GO DAG if Rgraphviz package is
    ##available.
    plotGOTermGraph(g=goDag(davidGODag), r=davidGODag, max.nchar=30,
    node.shape="ellipse")
    }

[Package RDAVIDWebService version 1.24.0 Index]