Basic summary for DAVIDWebService package classes.

Description

The different implementations of summary function for the DAVIDWebService package classes.

Usage

  summary(object, ...)

  ## S4 method for signature 'DAVIDCluster'
summary(object)

  ## S4 method for signature 'DAVIDGODag'
summary(object, ...)

  ## S4 method for signature 'DAVIDWebService'
summary(object)

Arguments

Value

data.frame with summary output.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDCluster: DAVIDCluster-class, cluster, cluster, dictionary, dictionary, enrichment, enrichment, members, members, membership, membership, subset, subset

Other DAVIDGODag: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGODag-class, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, benjaminis, benjaminis, bonferronis, bonferronis, counts, counts, fdrs, fdrs, foldEnrichments, foldEnrichments, initialize, initialize, initialize, initialize, initialize, initialize, initialize, listTotals, listTotals, percentages, percentages, popHits, popHits, popTotals, popTotals, terms, terms, universeCounts, universeMappedCount, upsideDown, upsideDown

Other DAVIDWebService: DAVIDWebService-class, addList, addList, connect, connect, getAllAnnotationCategoryNames, getAllAnnotationCategoryNames, getAnnotationSummary, getAnnotationSummary, getBackgroundListNames, getBackgroundListNames, getClusterReport, getClusterReport, getClusterReportFile, getClusterReportFile, getCurrentBackgroundListPosition, getCurrentBackgroundListPosition, getCurrentGeneListPosition, getCurrentGeneListPosition, getCurrentSpeciesPosition, getCurrentSpeciesPosition, getDefaultCategoryNames, getDefaultCategoryNames, getEmail, getEmail, getFunctionalAnnotationChart, getFunctionalAnnotationChart, getFunctionalAnnotationChartFile, getFunctionalAnnotationChartFile, getFunctionalAnnotationTable, getFunctionalAnnotationTable, getFunctionalAnnotationTableFile, getFunctionalAnnotationTableFile, getGeneCategoriesReport, getGeneCategoriesReport, getGeneListNames, getGeneListNames, getGeneListReport, getGeneListReport, getGeneListReportFile, getGeneListReportFile, getIdTypes, getIdTypes, getListName, getListName, getSpecieNames, getSpecieNames, getStub, getStub, is.connected, is.connected, setAnnotationCategories, setAnnotationCategories, setCurrentBackgroundPosition, setCurrentBackgroundPosition(position), setCurrentGeneListPosition, setCurrentGeneListPosition, setCurrentSpecies, setCurrentSpecies, setEmail, setEmail, setEmail,DAVIDWebService-method

Examples

{
##DAVIDGODag example:
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDGODag object using
##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
##obtained from the loaded data.frame funChart2. In addition, we have
##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
##DAVID/GO.db database are not using the same version.
data(funChart2)
davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
pvalueCutoff=0.001, removeUnattached=TRUE)
summary(davidGODag)


##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
summary(davidGeneCluster1)


##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
summary(davidTermCluster2)
}

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-summary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary
> ### Title: Basic summary for DAVIDWebService package classes.
> ### Aliases: summary,DAVIDCluster-method summary,DAVIDGODag-method
> ###   summary,DAVIDWebService-method summary
> 
> ### ** Examples
> 
> {
+ ##DAVIDGODag example:
+ ##Load the Functional Annotation Chart file report for the input demo
+ ##file 2, using data function. Then, create a DAVIDGODag object using
+ ##Molecular Function main category of DAVIDFunctionalAnnotationChart object,
+ ##obtained from the loaded data.frame funChart2. In addition, we have
+ ##selected a threshold pvalue of 0.001 and removed unattached nodes, in case
+ ##DAVID/GO.db database are not using the same version.
+ data(funChart2)
+ davidGODag<-DAVIDGODag(DAVIDFunctionalAnnotationChart(funChart2), type="MF",
+ pvalueCutoff=0.001, removeUnattached=TRUE)
+ summary(davidGODag)
+ 
+ 
+ ##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
+ summary(davidGeneCluster1)
+ 
+ 
+ ##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
+ summary(davidTermCluster2)
+ }
   Cluster Enrichment Members
1        1  6.6246712       5
2        2  4.9280032      14
3        3  3.4029820      17
4        4  3.0437847      11
5        5  3.0395873      14
6        6  2.6534403       4
7        7  2.6072640      39
8        8  2.2353363       6
9        9  2.0939417      35
10      10  2.0644910     112
11      11  1.9943655       5
12      12  1.9330485       7
13      13  1.9327385      19
14      14  1.8799262      11
15      15  1.8575128      11
16      16  1.8048680       6
17      17  1.7842250      11
18      18  1.6808208     149
19      19  1.6681540       8
20      20  1.5765837      12
21      21  1.5712490      28
22      22  1.4729089       5
23      23  1.4333903       7
24      24  1.3927567      25
25      25  1.3326134       5
26      26  1.2939364       6
27      27  1.2369302       4
28      28  1.2264852       7
29      29  1.1690170      30
30      30  1.1487065       5
31      31  1.0936003      27
32      32  1.0802862       5
33      33  1.0322953       7
34      34  0.9829631      18
35      35  0.9793807       9
36      36  0.9640336      17
37      37  0.9347984       8
38      38  0.9234716       8
39      39  0.8916268      20
40      40  0.8385261      16
41      41  0.7749948       4
42      42  0.7687626      12
43      43  0.7646703      11
44      44  0.7232982       5
45      45  0.6941567       4
46      46  0.6933980      17
47      47  0.6422416      46
48      48  0.6281064       4
49      49  0.6230012      18
50      50  0.6226999       4
51      51  0.4098024      34
52      52  0.3868265      10
53      53  0.3328992       5
54      54  0.2531608       6
55      55  0.2320971       5
56      56  0.2163833      14
57      57  0.1846742       6
58      58  0.1831802       5
59      59  0.1540890       6
60      60  0.1002034      16
61      61  0.0677913       4
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>