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Last data update: 2014.03.03

R: 'ids' for the different DAVIDWebService package class objects

ids	R Documentation

`ids` for the different DAVIDWebService package class objects

Description

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

Usage

  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

Examples

{
##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]]
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RDAVIDWebService)
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GOstats
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand



Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: ggplot2

Attaching package: 'RDAVIDWebService'

The following object is masked from 'package:AnnotationDbi':

    species

The following object is masked from 'package:IRanges':

    members

The following objects are masked from 'package:BiocGenerics':

    counts, species

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RDAVIDWebService/DAVIDClasses-ids.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ids
> ### Title: 'ids' for the different DAVIDWebService package class objects
> ### Aliases: ids,DAVIDFunctionalAnnotationChart-method
> ###   ids,DAVIDGeneCluster-method ids,DAVIDGenes-method
> ###   ids,DAVIDTermCluster-method ids
> 
> ### ** Examples
> 
> {
+ ##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]]
+ }
[[1]]
 [1] "2036_S_AT"  "430_AT"     "1520_S_AT"  "1953_AT"    "875_G_AT"  
 [6] "1388_G_AT"  "38374_AT"   "31737_AT"   "37233_AT"   "32583_AT"  
[11] "39372_AT"   "32464_AT"   "32779_S_AT" "1829_AT"    "1936_S_AT" 
[16] "39573_AT"   "259_S_AT"   "36674_AT"   "36101_S_AT" "224_AT"    
[21] "36100_AT"   "37310_AT"   "41216_R_AT" "35372_R_AT" "34666_AT"  
[26] "34981_AT"   "33802_AT"   "36009_AT"   "1973_S_AT"  "35345_AT"  
[31] "1548_S_AT"  "706_AT"     "1852_AT"    "35471_G_AT" "164_AT"    
[36] "1788_S_AT"  "1602_AT"    "37724_AT"   "39408_AT"   "2082_S_AT" 
[41] "36621_AT"   "31615_I_AT" "1461_AT"    "39402_AT"   "1939_AT"   
[46] "37606_AT"   "36519_AT"   "41169_AT"   "41726_AT"   "1007_S_AT" 
[51] "41234_AT"   "33092_AT"   "1895_AT"    "34375_AT"   "189_S_AT"  
[56] "33455_AT"   "37206_AT"   "41445_AT"   "34145_AT"   "1369_S_AT" 
[61] "36760_AT"   "1005_AT"    "31562_AT"   "1125_S_AT"  "408_AT"    
[66] "37365_AT"   "40385_AT"   "967_G_AT"   "36651_AT"   "568_AT"    
[71] "789_AT"     "40522_AT"   "37440_AT"   "36615_AT"   "41717_AT"  
[76] "40310_AT"   "40661_AT"   "36103_AT"   "1091_AT"   

[[2]]
 [1] "2036_S_AT"  "35149_AT"   "1520_S_AT"  "875_G_AT"   "31737_AT"  
 [6] "1388_G_AT"  "1148_S_AT"  "37233_AT"   "32583_AT"   "39372_AT"  
[11] "32464_AT"   "1936_S_AT"  "36674_AT"   "40669_AT"   "259_S_AT"  
[16] "37310_AT"   "32718_AT"   "1569_R_AT"  "35372_R_AT" "34666_AT"  
[21] "32928_AT"   "33802_AT"   "1973_S_AT"  "35345_AT"   "1548_S_AT" 
[26] "1852_AT"    "919_AT"     "40790_AT"   "39408_AT"   "37724_AT"  
[31] "1372_AT"    "36621_AT"   "31615_I_AT" "39402_AT"   "1939_AT"   
[36] "41169_AT"   "41088_AT"   "33092_AT"   "1895_AT"    "34375_AT"  
[41] "189_S_AT"   "1139_AT"    "33455_AT"   "33825_AT"   "41445_AT"  
[46] "34145_AT"   "1369_S_AT"  "36760_AT"   "1005_AT"    "31562_AT"  
[51] "2004_AT"    "39753_AT"   "1125_S_AT"  "41387_R_AT" "408_AT"    
[56] "40385_AT"   "37440_AT"   "41717_AT"   "40310_AT"   "40661_AT"  
[61] "36103_AT"  

[[3]]
 [1] "2036_S_AT"  "36621_AT"   "31615_I_AT" "35149_AT"   "1520_S_AT" 
 [6] "39402_AT"   "875_G_AT"   "1148_S_AT"  "37233_AT"   "41169_AT"  
[11] "41088_AT"   "34375_AT"   "189_S_AT"   "36674_AT"   "259_S_AT"  
[16] "40669_AT"   "1139_AT"    "37310_AT"   "33825_AT"   "32718_AT"  
[21] "34145_AT"   "1369_S_AT"  "41445_AT"   "1569_R_AT"  "35372_R_AT"
[26] "36760_AT"   "2004_AT"    "39753_AT"   "34666_AT"   "32928_AT"  
[31] "33802_AT"   "1125_S_AT"  "41387_R_AT" "408_AT"     "40385_AT"  
[36] "1548_S_AT"  "1852_AT"    "40310_AT"   "36103_AT"   "919_AT"    
[41] "1372_AT"   

[[4]]
 [1] "2036_S_AT"  "35149_AT"   "1520_S_AT"  "1953_AT"    "37584_AT"  
 [6] "36711_AT"   "274_AT"     "875_G_AT"   "1148_S_AT"  "37233_AT"  
[11] "32583_AT"   "39372_AT"   "32464_AT"   "32779_S_AT" "1829_AT"   
[16] "39573_AT"   "35956_S_AT" "259_S_AT"   "40669_AT"   "36674_AT"  
[21] "36101_S_AT" "36100_AT"   "37310_AT"   "32718_AT"   "1569_R_AT" 
[26] "35372_R_AT" "36226_R_AT" "34666_AT"   "32928_AT"   "34981_AT"  
[31] "33802_AT"   "36009_AT"   "41371_AT"   "1548_S_AT"  "1852_AT"   
[36] "38970_S_AT" "35471_G_AT" "41099_AT"   "41382_AT"   "919_AT"    
[41] "1372_AT"    "39408_AT"   "36621_AT"   "31615_I_AT" "34226_AT"  
[46] "39402_AT"   "1939_AT"    "36519_AT"   "41169_AT"   "41726_AT"  
[51] "41234_AT"   "41088_AT"   "1258_S_AT"  "1895_AT"    "34375_AT"  
[56] "189_S_AT"   "1139_AT"    "33455_AT"   "33825_AT"   "41445_AT"  
[61] "34145_AT"   "1369_S_AT"  "1857_AT"    "36760_AT"   "1005_AT"   
[66] "39753_AT"   "2004_AT"    "32405_AT"   "1125_S_AT"  "41387_R_AT"
[71] "408_AT"     "35957_AT"   "37365_AT"   "31522_F_AT" "41106_AT"  
[76] "1911_S_AT"  "40385_AT"   "967_G_AT"   "33698_AT"   "36615_AT"  
[81] "41717_AT"   "40310_AT"   "36103_AT"   "652_G_AT"  

[[5]]
  [1] "1520_S_AT"  "1953_AT"    "274_AT"     "875_G_AT"   "1388_G_AT" 
  [6] "31737_AT"   "38374_AT"   "32583_AT"   "39372_AT"   "1829_AT"   
 [11] "39573_AT"   "35956_S_AT" "36674_AT"   "259_S_AT"   "36100_AT"  
 [16] "41216_R_AT" "38018_G_AT" "35372_R_AT" "36226_R_AT" "34666_AT"  
 [21] "32928_AT"   "33802_AT"   "36009_AT"   "1973_S_AT"  "41371_AT"  
 [26] "35345_AT"   "1548_S_AT"  "706_AT"     "164_AT"     "41099_AT"  
 [31] "1788_S_AT"  "41382_AT"   "40790_AT"   "31615_I_AT" "39402_AT"  
 [36] "1461_AT"    "1939_AT"    "37606_AT"   "33012_AT"   "41169_AT"  
 [41] "1385_AT"    "33092_AT"   "34375_AT"   "33455_AT"   "1369_S_AT" 
 [46] "34145_AT"   "1857_AT"    "36760_AT"   "31562_AT"   "1005_AT"   
 [51] "2004_AT"    "32405_AT"   "31586_F_AT" "39424_AT"   "408_AT"    
 [56] "35957_AT"   "41106_AT"   "36651_AT"   "33698_AT"   "37440_AT"  
 [61] "40522_AT"   "31564_AT"   "40661_AT"   "36103_AT"   "2036_S_AT" 
 [66] "471_F_AT"   "430_AT"     "35149_AT"   "36711_AT"   "37584_AT"  
 [71] "38538_AT"   "1148_S_AT"  "37233_AT"   "32464_AT"   "32779_S_AT"
 [76] "33094_S_AT" "1936_S_AT"  "40669_AT"   "36101_S_AT" "224_AT"    
 [81] "37310_AT"   "36669_AT"   "32718_AT"   "1569_R_AT"  "1919_AT"   
 [86] "37418_AT"   "34981_AT"   "37139_AT"   "833_AT"     "38970_S_AT"
 [91] "1852_AT"    "35471_G_AT" "612_S_AT"   "1263_AT"    "1602_AT"   
 [96] "919_AT"     "2082_S_AT"  "39408_AT"   "37724_AT"   "1372_AT"   
[101] "36621_AT"   "34226_AT"   "36519_AT"   "41726_AT"   "1007_S_AT" 
[106] "41234_AT"   "41088_AT"   "1258_S_AT"  "1244_AT"    "1895_AT"   
[111] "189_S_AT"   "1139_AT"    "37206_AT"   "33825_AT"   "41445_AT"  
[116] "39753_AT"   "32696_AT"   "1125_S_AT"  "37317_AT"   "41387_R_AT"
[121] "33555_AT"   "37365_AT"   "31522_F_AT" "1911_S_AT"  "40385_AT"  
[126] "967_G_AT"   "568_AT"     "789_AT"     "37857_AT"   "36615_AT"  
[131] "41717_AT"   "40310_AT"   "1091_AT"    "652_G_AT"   "31977_AT"  

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

ids for the different DAVIDWebService package class objects