DAVIDFunctionalAnnotationChart-class {RDAVIDWebService} | R Documentation

## class "DAVIDFunctionalAnnotationChart

### Description

This class represents the output of "Functional Annotation Chart" of DAVID. It is an heir of DAVIDResult in the conceptual way, and also a data.frame with additional features, such as identifying the unique and duplicate ids, searching for genes with a given id, etc.

### Type

This class is a "`Concrete`" one.

### Extends

- DAVIDResult in the conceptual way.

- data.frame in order to extend the basic features.

### Slots

no additional to the ones inherited from DAVIDResult and data.frame classes.

### Methods

`show`

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

`valid`

  `signature(object="DAVIDFunctionalAnnotationChart")` : logical which checks DAVID's file output name ("Category", "Term", "Count", etc.) presence.

`DAVIDFunctionalAnnotationChart`

  `signature( object="character")`: constructor with the name of the .tab file report to load.

`DAVIDFunctionalAnnotationChart`

  `signature( object="data.frame")`: data.frame already loaded to use when constructing the object.

`as`

  `signature(object="DAVIDFunctionalAnnotationChart")`: coerce a data.frame into a DAVIDFunctionalAnnotationChart object.

`categories`

  `signature( object="DAVIDFunctionalAnnotationChart")`: obtain the factor vector of the "Category" column.

`ids`

  `signature(object="DAVIDFunctionalAnnotationChart")`: obtain a list with character/integer vector with the ids of the corresponding term.

### 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 DAVIDFunctionalAnnotationChart: `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationChart`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDFunctionalAnnotationTable`, `DAVIDGODag`, `DAVIDGODag`, `DAVIDGeneCluster`, `DAVIDGeneCluster`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDGenes`, `DAVIDTermCluster`, `DAVIDTermCluster`, `as`, `as`, `as`, `categories`, `categories`, `categories`, `ids`, `ids`, `ids`, `ids`, `ids`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `initialize`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`, `plot2D`

### Examples

    {
    ##Load the Functional Annotation Chart file report for the input demo
    ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
    ## object using the loaded data.frame funChart2. In addition, the user can
    ##use the file name of the downloaded file report.
    data(funChart2)
    davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)

    ##In Addition to the usual data.frame accessors, the user can inspect the
    ##main categories used in the analysis.
    categories(davidFunChart2)

    ##Obtain the ids of the genes present in each Term, as a list of character
    ##vector
    ids(davidFunChart2)

    ##Or plot a 2D tile matrix with the reported evidence (green) or not (black).
    ##Just to keep it simple, for the first five terms present in funChart2
    ##object.
    plot2D(DAVIDFunctionalAnnotationChart(funChart2[1:5, ]),
    color=c("FALSE"="black", "TRUE"="green"))
    }

[Package RDAVIDWebService version 1.18.0 Index]