DAVIDGODag-methods: Methods for 'DAVIDGODag' class object

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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  terms(x, ...)

  ## S4 method for signature 'DAVIDGODag'
terms(x, ...)

  percentages(object)

  ## S4 method for signature 'DAVIDGODag'
percentages(object)

  listTotals(object)

  ## S4 method for signature 'DAVIDGODag'
listTotals(object)

  popHits(object)

  ## S4 method for signature 'DAVIDGODag'
popHits(object)

  popTotals(object)

  ## S4 method for signature 'DAVIDGODag'
popTotals(object)

  foldEnrichments(object)

  ## S4 method for signature 'DAVIDGODag'
foldEnrichments(object)

  bonferronis(object)

  ## S4 method for signature 'DAVIDGODag'
bonferronis(object)

  benjaminis(object)

  ## S4 method for signature 'DAVIDGODag'
benjaminis(object)

  fdrs(object)

  ## S4 method for signature 'DAVIDGODag'
fdrs(object)

  counts(object, ...)

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

  upsideDown(graph)

  ## S4 method for signature 'graph'
upsideDown(graph)

  ## S4 method for signature 'DAVIDGODag'
universeCounts(r)

  ## S4 method for signature 'DAVIDGODag'
universeMappedCount(r)

Arguments

object,x,r

DAVIDGODag class object.

graph

a graph object with the GO DAG structure.

...

Additional parameters (if required).

Value

according to the call one of the following objects can be returned

upsideDown

the same graph but the arcs with its directions in the other way around. Hence, plot layout would make upside down the graph.

universeMappedCount, universeCounts, counts

modifications to the corresponding GOstats/Category library functions, to keep the same behavior for DAVIDGODag objects.

fdrs, benjaminis, bonferronis

Adjusted method specific p-values for the corresponding nodes/terms.

terms

character vector with GO node names.

popTotals, popHits, listTotals

integer vector with the number of ids, to use in the EASE score calculations, when building the 2x2 contingency table.

percentages

numeric vector with the percentage of the gene list ids present in the term.

foldEnrichments

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

See Also

Other DAVIDGODag: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGODag-class, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, initialize, initialize, initialize, initialize, initialize, initialize, initialize, summary, summary, summary, summary

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)
}

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