DAVIDFunctionalAnnotationTable-class {RDAVIDWebService} | R Documentation

## class "DAVIDFunctionalAnnotationTable

### Description

This class represents the output of a DAVID Functional Annotation Table report. In this class no statistical analysis is carried out.

### Type

This class is a "`Concrete`" one.

### Extends

- DAVIDResult in the conceptual way, and to reuse some functionalities such as plot2D, type and so on.

### Slots

`Genes`

  a DAVIDGenes object with the submitted genes.

`Dictionary`

  a look up list of data.frame of each main annotation category, where the specified IDs and Terms used can be found.

`Membership`

  list with logical membership matrix, where gene ids are coded by rows and the respective annotation category ids as columns.

### Methods

`initialize`

  `signature(.Object= "DAVIDFunctionalAnnotationTable", fileName="character")`: basic Functional Annotation Table report file parser.

`DAVIDFunctionalAnnotationTable`

  `signature(fileName= "character")`: high level Functional Annotation Table report file parser.

`valid`

  `signature(object= "DAVIDFunctionalAnnotationTable")`:logical which checks for Membership, Dictionary and Genes cohesion.

`show`

  `signature(object="DAVIDFunctionalAnnotationTable")`: returns a basic console output.

`genes`

  `signature(object="DAVIDFunctionalAnnotationTable")` : returns a DAVIDGenes object.

`subset`

  `signature(object= "DAVIDFunctionalAnnotationTable", selection=c("Membership","Dictionary"), category, drop=TRUE)`: returns a subset list using the selection slot, looking up the category parameter if provided. Otherwise, it returns all the available main categories. Drop parameter indicates whether to drop list structure or not, if a list of length==1 is to be returned.

`dictionary`

  `signature(object= "DAVIDFunctionalAnnotationTable", category, drop=TRUE)`: returns subset using selection="Dictionary" and category and drop parameters.

`membership`

  `signature(object= "DAVIDFunctionalAnnotationTable", category="character", drop=TRUE)`: returns subset using selection="Membership" and category and drop parameters.

`genes`

  `signature(object= "DAVIDFunctionalAnnotationTable", ...)`: returns a DAVIDGenes object slot, according to additional ... parameters.

`categories`

  `signature(object= "DAVIDFunctionalAnnotationTable")`: returns a character vector with the main annotation categories available..

`plot2D`

  `signature(object="DAVIDFunctionalAnnotationTable", category, id, names.genes=FALSE, names.category=FALSE, color=c("FALSE"="black", "TRUE"="green"))`: ggplot2 tile plot of genes id vs functional annotation category membership. If missing, all available data is used. In addition, names.genes and names.category parameters indicate whether to use or not, genes and category names respectively. Default value is FALSE.

### 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

### See Also

Other DAVIDFunctionalAnnotationTable: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `categories`, `categories`, `categories`, `dictionary`, `dictionary`, `genes`, `genes`, `genes`, `genes`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `membership`, `membership`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `subset`, `subset`

### Examples

    {
    ##Load the Functional Annotation Table file report for the input demo
    ##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
    ##object using the loaded data.frame annotationTable1. In addition, the user
    ##can use the file name of the downloaded file report.
    data(annotationTable1)
    davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)

    ##Now we can obtain the genes for the given ids, or the complete list if the
    ##parameter is omitted.
    genes(davidFunTable1, id=c("37166_at","41703_r_at"))

    ##Or the main categories used on the analysis, in order to get the
    ##dictionary for a specific category (ID and Term fields), for the head of
    ##the data.frame.
    categories(davidFunTable1)
    head(dictionary(davidFunTable1, categories(davidFunTable1)[1]))

    ##And what about the membership of the genes in these terms? Just for the
    ##first six ids we can use:
    head(membership(davidFunTable1, categories(davidFunTable1)[1]))

    ##Or simply plot the membership of only for the first six terms in this
    ##category, with only the genes of the first six terms with at least one
    ##evidence code.
    ##Category filtering...
    categorySelection<-list(head(dictionary(davidFunTable1,
    categories(davidFunTable1)[1])$ID))
    names(categorySelection)<-categories(davidFunTable1)[1]

    ##Gene filter...
    id<-membership(davidFunTable1, categories(davidFunTable1)[1])[,1:6]
    id<-ids(genes(davidFunTable1))[rowSums(id)>0]

    ##Finally the membership tile plot
    plot2D(davidFunTable1, category=categorySelection, id=id,
    names.category=TRUE)
    }

[Package RDAVIDWebService version 1.18.0 Index]