class "DAVIDGODag

Description

This concrete class represents an induced GO DAG generated by the DAVID Functional Annotation Chart report a.k.a a DAVIDFunctionalAnnotationChart object.

Type

This class is a "Concrete" one.

Extends

• GOHyperGResult directly, in order to reuse GOstats functionalities.

Slots

the ones inherited from GOHyperGResult

Methods

show

signature(object="DAVIDGODag"): basic console output.

summary

signature(object="DAVIDGODag", ...): basic summary console output.

initialize

signature(object="DAVIDGODag", fileName="character"): basic cluster report file parser.

DAVIDGODag

signature(object="DAVIDGODag", fileName="character"): high level constructor to parse the file report.

universeMappedCount, universeCounts, counts

signature( object="DAVIDGODag"): modifications to the corresponding GOstats/Category library functions, to keep the same behavior, for DAVIDGODag object.

fdrs, benjaminis, bonferronis

signature( object="DAVIDGODag"): Adjusted method specific p-values for the corresponding nodes/terms.

terms

signature(object="DAVIDGODag"): character vector with GO node names.

popTotals, popHits, listTotals

signature( object="DAVIDGODag"): integer vector with the number of ids, to use in the EASE score calculations, when building the 2x2 contingency table.

percentages

signature(object="DAVIDGODag"): numeric vector with the percentage of the gene list ids present in the term.

foldEnrichments

signature(object="DAVIDGODag"):numeric vector with the ratio of the two proportions for each node/term. For example, if 40/400 (i.e. 10%) of your input genes involved in "kinase activity" and the background information is 300/30000 genes (i.e. 1%) associating with "kinase activity", roughly 10%/1%=10 fold enrichment.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

3. Falcon, S; Gentleman, R.; Using GOstats to test gene lists for GO term association, Bioinformatics 23 (2007) 257-258.

See Also

Other DAVIDGODag: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, 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, summary, summary, summary, summary, terms, terms, universeCounts, universeMappedCount, upsideDown, upsideDown

Examples

{
##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)

##Now, we can inspect the enrichment GO DAG using GOstats functionalities:
##counts, pvalues, sigCategories, universeCounts, geneMappedCount, etc.
##However, oddsRatios, expectedCounts and universeMappedCount are not
##available because these results are not available on DAVID's Functional
##Annotation Chart report. In addition geneIdUniverse are not the ones of
##the universe but the ids on the category (geneIdsByCategory).
davidGODag
counts(davidGODag)
pvalues(davidGODag)
sigCategories(davidGODag, p=0.0001)
universeCounts(davidGODag)
geneMappedCount(davidGODag)
geneIdsByCategory(davidGODag)
summary(davidGODag)

##In addition, the new nodeData attributes (term, listTotal, popHit,
##popTotal, foldEnrichment, bonferroni, benjamini, fdr) can be retrieved.
terms(davidGODag)
listTotals(davidGODag)
popHits(davidGODag)
popTotals(davidGODag)
foldEnrichments(davidGODag)
bonferronis(davidGODag)
benjaminis(davidGODag)
fdrs(davidGODag)

##The user can even plot the enrichment GO DAG if Rgraphviz package is
##available.
plotGOTermGraph(g=goDag(davidGODag), r=davidGODag, max.nchar=30,
node.shape="ellipse")
}

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/DAVIDGODag-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DAVIDGODag-class
> ### Title: class "DAVIDGODag
> ### Aliases: DAVIDGODag-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> {
+ ##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)
+ 
+ ##Now, we can inspect the enrichment GO DAG using GOstats functionalities:
+ ##counts, pvalues, sigCategories, universeCounts, geneMappedCount, etc.
+ ##However, oddsRatios, expectedCounts and universeMappedCount are not
+ ##available because these results are not available on DAVID's Functional
+ ##Annotation Chart report. In addition geneIdUniverse are not the ones of
+ ##the universe but the ids on the category (geneIdsByCategory).
+ davidGODag
+ counts(davidGODag)
+ pvalues(davidGODag)
+ sigCategories(davidGODag, p=0.0001)
+ universeCounts(davidGODag)
+ geneMappedCount(davidGODag)
+ geneIdsByCategory(davidGODag)
+ summary(davidGODag)
+ 
+ ##In addition, the new nodeData attributes (term, listTotal, popHit,
+ ##popTotal, foldEnrichment, bonferroni, benjamini, fdr) can be retrieved.
+ terms(davidGODag)
+ listTotals(davidGODag)
+ popHits(davidGODag)
+ popTotals(davidGODag)
+ foldEnrichments(davidGODag)
+ bonferronis(davidGODag)
+ benjaminis(davidGODag)
+ fdrs(davidGODag)
+ 
+ ##The user can even plot the enrichment GO DAG if Rgraphviz package is
+ ##available.
+ plotGOTermGraph(g=goDag(davidGODag), r=davidGODag, max.nchar=30,
+ node.shape="ellipse")
+ }

Attaching package: 'Rgraphviz'

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

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

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