| species {RDAVIDWebService} | R Documentation |
DAVIDGenes class objectObtain DAVIDGenes related information, according to the given function call (see Values).
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)
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). |
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. |
Cristobal Fresno and Elmer A Fernandez
{
##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)
}