DAVIDGODag-class: class "DAVIDGODag

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

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

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

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{
##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")
}

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