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) }