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) }