DAVIDFunctionalAnnotationChart-class: class "DAVIDFunctionalAnnotationChart
In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description Type Extends Slots Methods Author(s) References See Also Examples

This class represents the output of "Functional Annotation Chart" of DAVID. It is an heir of DAVIDResult in the conceptual way, and also a data.frame with additional features, such as identifying the unique and duplicate ids, searching for genes with a given id, etc.

This class is a "Concrete" one.

DAVIDResult in the conceptual way.
data.frame in order to extend the basic features.

no additional to the ones inherited from DAVIDResult and data.frame classes.

show: signature(object="DAVIDFunctionalAnnotationChart"): returns a basic console output.
valid: signature(object="DAVIDFunctionalAnnotationChart") : logical which checks DAVID's file output name ("Category", "Term", "Count", etc.) presence.
DAVIDFunctionalAnnotationChart: signature( object="character"): constructor with the name of the .tab file report to load.
DAVIDFunctionalAnnotationChart: signature( object="data.frame"): data.frame already loaded to use when constructing the object.
as: signature(object="DAVIDFunctionalAnnotationChart"): coerce a data.frame into a DAVIDFunctionalAnnotationChart object.
categories: signature( object="DAVIDFunctionalAnnotationChart"): obtain the factor vector of the "Category" column.
ids: signature(object="DAVIDFunctionalAnnotationChart"): obtain a list with character/integer vector with the ids of the corresponding term.

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 DAVIDFunctionalAnnotationChart: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, categories, categories, categories, ids, ids, ids, ids, ids, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

{
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
## object using the loaded data.frame funChart2. In addition, the user can
##use the file name of the downloaded file report.
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)

##In Addition to the usual data.frame accessors, the user can inspect the
##main categories used in the analysis.
categories(davidFunChart2)

##Obtain the ids of the genes present in each Term, as a list of character
##vector
ids(davidFunChart2)

##Or plot a 2D tile matrix with the reported evidence (green) or not (black).
##Just to keep it simple, for the first five terms present in funChart2
##object.
plot2D(DAVIDFunctionalAnnotationChart(funChart2[1:5, ]),
color=c("FALSE"="black", "TRUE"="green"))
}

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