DAVIDClasses-ids: 'ids' for the different DAVIDWebService package class objects

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
  ids(object)

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

  ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
ids(object)

  ## S4 method for signature 'DAVIDGeneCluster'
ids(object)

  ## S4 method for signature 'DAVIDTermCluster'
ids(object)

Arguments

object

DAVIDWebService class object. Possible values are: DAVIDGenes, DAVIDFunctionalAnnotationChart, DAVIDGeneCluster or DAVIDTermCluster.

Value

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

DAVIDGenes

character vector with gene submitted ids.

DAVIDFunctionalAnnotationChart

list with character/integer vector of ids of the corresponding "Category".

DAVIDGeneCluster, DAVIDTermCluster

list with character/integer vector of ids of the members of each cluster.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDFunctionalAnnotationChart: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart-class, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, categories, categories, categories, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Other DAVIDGeneCluster: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGeneCluster-class, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Other DAVIDGenes: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDGenes-class, DAVIDTermCluster, DAVIDTermCluster, as, as, as, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize

Other DAVIDTermCluster: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, DAVIDTermCluster-class, as, as, as, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
{
##DAVIDGenes example:
##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. Once, the report is loaded, we can retrieve the ids.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)
ids(davidGenes1)

##DAVIDFunctionalAnnotationChart example:
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
##object using the loaded data.frame funChart2. Once the report is loaded,
##the user can obtain the ids of the genes present in each Term, as a list of
##character vector.
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)
ids(davidFunChart2)


##DAVIDGeneCluster example:
##Load the Gene Functional Classification Tool file report for the
##input demo list 1 file to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))
davidGeneCluster1

##Now we can invoke DAVIDCluster ancestor functions to inspect the report
##data, of each cluster. For example, we can call summary to get a general
##idea, and the inspect the cluster with higher Enrichment Score, to see
##which members belong to it, etc. Or simply returning the whole cluster as
##a list with EnrichmentScore and Members.
summary(davidGeneCluster1)
higherEnrichment<-which.max(enrichment(davidGeneCluster1))
clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]]
wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]]

##Now, we can obtain the ids of the  first cluster directly using
##davidGeneCluster1 or by using DAVIDGenes class on the same cluster.
ids(davidGeneCluster1)[[1]]
ids(members(davidGeneCluster1)[[1]])


##DAVIDTermCluster example:
##Load the Gene Functional Classification Tool file report for the
##input demo file 2 to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/termClusterReport2.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
davidTermCluster2

##Now we can invoke DAVIDCluster ancestor functions to inspect the report
##data, of each cluster. For example, we can call summary to get a general
##idea, and the inspect the cluster with higher Enrichment Score, to see
##which members belong to it, etc. Or simply returning the whole cluster as a
##list with EnrichmentScore and Members.
summary(davidTermCluster2)
higherEnrichment<-which.max(enrichment(davidTermCluster2))
clusterGenes<-members(davidTermCluster2)[[higherEnrichment]]
wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]]

##Then, we can obtain the ids of the term members calling clusterGenes object
##which is a DAVIDFunctionalAnnotationChart class or directly using ids on
##davidTermCluster2 for the higherEnrichment cluster.
ids(clusterGenes)
ids(davidTermCluster2)[[higherEnrichment]]
}

Bioconductor-mirror/RDAVIDWebService documentation built on May 31, 2017, 10:42 p.m.