DAVIDGODag-class {RDAVIDWebService} | R Documentation |
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") }