RDAVIDWebService (version 1.10.0)

species: Methods for DAVIDGenes class object

Description

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

Usage

species(object)
  "species"(object)
  duplicateIds(object, collapse = FALSE)
  "duplicateIds"(object, collapse=FALSE)
  uniqueIds(object)
  "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.

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)
}