DAVIDGenes-class {RDAVIDWebService} | R Documentation

## class "DAVIDGenes

### Description

This class represents the output of "Show Genes Result" 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

none additional to the ones inherited from DAVIDResult and data.frame classes.

### Methods

`valid`

  `signature(object="DAVIDGenes")`: logical which checks for data.frame name (ID, Name) presence.

`DAVIDGenes`

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

`DAVIDGenes`

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

`ids`

  `signature(object="DAVIDGenes")`: character vector with gene submitted ids.

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

### Examples

    {
    ##Load Show Gene List file report for the input demo file 1, using data
    ##function. Then, create a DAVIDGenes object using the loaded data.frame
    ##geneList1. In addition, the user can use the file name of the downloaded
    ##file report.
    data(geneList1)
    davidGenes1<-DAVIDGenes(geneList1)

    ##Now we can inspect davidGenes1 as it was an common data.frame
    head(davidGenes1)

    ##Additional getters for this object are also available, to obtain the
    ##different columns: ids, genes and species.
    ids(davidGenes1)
    genes(davidGenes1)
    species(davidGenes1)

    ##Or even look up for a particular gene id, which will return only the
    ##matched ones.
    genes(davidGenes1, ids=c("38926_at", "35367_at", "no match"))

    ##Obtain the genes with duplicate manufacturer ids or just the genes that
    ##do not have duplicate ids (uniqueIds).
    duplicateIds(davidGenes1)
    uniqueIds(davidGenes1)
    }

[Package RDAVIDWebService version 1.24.0 Index]