species {RDAVIDWebService} | R Documentation

## Methods for `DAVIDGenes` class object

### Description

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

### Usage

      species(object)

      ## S4 method for signature 'DAVIDGenes'
    species(object)

      duplicateIds(object, collapse = FALSE)

      ## S4 method for signature 'DAVIDGenes'
    duplicateIds(object,
      collapse=FALSE)

      uniqueIds(object)

      ## S4 method for signature 'DAVIDGenes'
    uniqueIds(object)

### Arguments

`object` | DAVIDGenes class object.
`collapse` | logical indicating if duplicate ids should be grouped as a comma separated id. Default value is FALSE.
`...` | Additional parameters for internal functions (if applicable).

### Value

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

`show` | console output of the class and associated data.
`species` | character vector with the levels of Species if available.
`uniqueIds` | a DAVIDGenes object with only the gene names with a unique id.
`duplicateIds` | a DAVIDGenes object with only the gene names with at least two ids. If collapse is TRUE, a data.frame in where all the ids that matched the same gene name, are coded in comma separated style.

### Author(s)

Cristobal Fresno and Elmer A Fernandez

### 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 1.18.0 Index]