| terms {RDAVIDWebService} | R Documentation |
DAVIDGODag class objectObtain DAVIDGODag related information, according to the given function call (see Values).
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)
object,x,r |
DAVIDGODag class object. |
graph |
a graph object with the GO DAG structure. |
... |
Additional parameters (if required). |
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. |
Cristobal Fresno and Elmer A Fernandez
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
{
##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)
}