terms {RDAVIDWebService} | R Documentation

## Methods for `DAVIDGODag` class object

### Description

Obtain DAVIDGODag related information, according to the given function call (see Values).

### Usage

      terms(x, ...)

      ## S4 method for signature 'DAVIDGODag'
    terms(x, ...)

      percentages(object)

      ## S4 method for signature 'DAVIDGODag'
    percentages(object)

      listTotals(object)

      ## S4 method for signature 'DAVIDGODag'
    listTotals(object)

      popHits(object)

      ## S4 method for signature 'DAVIDGODag'
    popHits(object)

      popTotals(object)

      ## S4 method for signature 'DAVIDGODag'
    popTotals(object)

      foldEnrichments(object)

      ## S4 method for signature 'DAVIDGODag'
    foldEnrichments(object)

      bonferronis(object)

      ## S4 method for signature 'DAVIDGODag'
    bonferronis(object)

      benjaminis(object)

      ## S4 method for signature 'DAVIDGODag'
    benjaminis(object)

      fdrs(object)

      ## S4 method for signature 'DAVIDGODag'
    fdrs(object)

      counts(object, ...)

      ## S4 method for signature 'DAVIDGODag'
    counts(object, ...)

      upsideDown(graph)

      ## S4 method for signature 'graph'
    upsideDown(graph)

      ## S4 method for signature 'DAVIDGODag'
    universeCounts(r)

      ## S4 method for signature 'DAVIDGODag'
    universeMappedCount(r)

### Arguments

`object,x,r` | DAVIDGODag class object.
`graph` | a graph object with the GO DAG structure.
`...` | Additional parameters (if required).

### Value

according to the call one of the following objects can be returned

`upsideDown` | the same graph but the arcs with its directions in the other way around. Hence, plot layout would make upside down the graph.
`universeMappedCount, universeCounts, counts` | modifications to the corresponding GOstats/Category library functions, to keep the same behavior for DAVIDGODag objects.
`fdrs, benjaminis, bonferronis` | Adjusted method specific p-values for the corresponding nodes/terms.
`terms` | character vector with GO node names.
`popTotals, popHits, listTotals` | integer vector with the number of ids, to use in the EASE score calculations, when building the 2x2 contingency table.
`percentages` | numeric vector with the percentage of the gene list ids present in the term.
`foldEnrichments` | 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

### See Also

Other DAVIDGODag: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGODag-class`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `summary`, `summary`, `summary`, `summary`

### 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)
    }

[Package RDAVIDWebService version 1.26.0 Index]