DAVIDGeneCluster-class {RDAVIDWebService} | R Documentation |
This class represents the output of a DAVID Gene Functional Classification Tool report.
This class is a "Concrete
" one.
DAVIDCluster and uses its constructor to parse the report.
the ones inherited from DAVIDCluster.
initialize
signature(.Object="DAVIDGeneCluster",
fileName="character")
: basic cluster report file
parser.
DAVIDGeneCluster
signature(fileName="character")
:
high level gene cluster report file parser.
ids
signature(object="DAVIDGeneCluster")
:
list with the member ids within each cluster.
genes
signature(object="DAVIDGeneCluster")
:
list with the DAVIDGenes members within each cluster.
plot2D
signature(object="DAVIDGeneCluster",
color=c("FALSE"="black","TRUE"="green"), names=FALSE)
:
ggplot2 tile plot with gene membership to each cluster.
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 DAVIDGeneCluster:
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationChart
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDFunctionalAnnotationTable
,
DAVIDGODag
, DAVIDGODag
,
DAVIDGeneCluster
,
DAVIDGeneCluster
, DAVIDGenes
,
DAVIDGenes
, DAVIDGenes
,
DAVIDTermCluster
,
DAVIDTermCluster
, as
,
as
, as
, genes
,
genes
, genes
,
genes
, 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 list 1 file to create a DAVIDGeneCluster object. setwd(tempdir()) fileName<-system.file("files/geneClusterReport1.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE)) davidGeneCluster1 ##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(davidGeneCluster1) higherEnrichment<-which.max(enrichment(davidGeneCluster1)) clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]] wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]] ##Then, we can obtain the ids of the members calling clusterGenes object ##which is a DAVIDGenes class or directly using ids on davidGeneCluster1. ids(clusterGenes) ids(davidGeneCluster1)[[higherEnrichment]] ##Obtain the genes of the first cluster using davidGeneCluster1 object. ##Or, using genes on DAVIDGenes class once we get the members of the cluster. genes(davidGeneCluster1)[[1]] genes(members(davidGeneCluster1)[[1]]) ##Finally, we can inspect a 2D tile membership plot, to visually inspect for ##overlapping of genes across the clusters. Or use a scaled version of gene ##names to see the association of gene cluster, e.g., cluster 3 is related to ##ATP genes. plot2D(davidGeneCluster1) plot2D(davidGeneCluster1,names=TRUE)+ theme(axis.text.y=element_text(size=rel(0.9))) }