DAVIDTermCluster-class {RDAVIDWebService} | R Documentation |
This class represents the output of a DAVID Functional Annotation Clustering report.
This class is a "Concrete
" one.
DAVIDCluster and uses its constructor to parse the report.
the ones inherited from DAVIDCluster.
initialize
signature(.Object="DAVIDTermCluster",
fileName="character")
: basic cluster report file
parser.
DAVIDTermCluster
signature(fileName="character")
:
high level gene cluster report file parser.
ids
signature(object="DAVIDTermCluster")
:
list with the member ids within each cluster.
plot2D
signature(object="DAVIDTermCluster",
number=1, color=c("FALSE"="black","TRUE"="green"))
:
ggplot2 tile plot of genes vs functional annotation
category membership of the given cluster number.
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
Other DAVIDTermCluster:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
, ids
,
ids
, ids
, ids
,
ids
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
initialize
, initialize
,
plot2D
, plot2D
,
plot2D
, plot2D
,
plot2D
, plot2D
{ ##Load the Gene Functional Classification Tool file report for the ##input demo file 2 to create a DAVIDGeneCluster object. setwd(tempdir()) fileName<-system.file("files/termClusterReport2.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE)) davidTermCluster2 ##Now we can invoke DAVIDCluster ancestor functions to inspect the report ##data, of each cluster. For example, we can call summary to get a general ##idea, and the inspect the cluster with higher Enrichment Score, to see ##which members belong to it, etc. Or simply returning the whole cluster as a ##list with EnrichmentScore and Members. summary(davidTermCluster2) higherEnrichment<-which.max(enrichment(davidTermCluster2)) clusterGenes<-members(davidTermCluster2)[[higherEnrichment]] wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]] ##Then, we can obtain the ids of the term members calling clusterGenes object ##which is a DAVIDFunctionalAnnotationChart class or directly using ids on ##davidTermCluster2 for the higherEnrichment cluster. ids(clusterGenes) ids(davidTermCluster2)[[higherEnrichment]] ##Finally, we can inspect a 2D tile membership plot, to visual inspect for ##overlapping of genes across the term members of the selected cluster. plot2D(davidTermCluster2, number=higherEnrichment) }