DAVIDGODag-class: class "DAVIDGODag
In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description Type Extends Slots Methods Author(s) References See Also Examples

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

This class is a "Concrete" one.

GOHyperGResult directly, in order to reuse GOstats functionalities.

the ones inherited from GOHyperGResult

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.

Cristobal Fresno and Elmer A Fernandez

The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)
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
Falcon, S; Gentleman, R.; Using GOstats to test gene lists for GO term association, Bioinformatics 23 (2007) 257-258.

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

{
##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")
}