class "DAVIDFunctionalAnnotationChart

Description

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.

Type

This class is a "Concrete" one.

Extends

• DAVIDResult in the conceptual way.

• data.frame in order to extend the basic features.

Slots

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

Methods

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.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. 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

See Also

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

Examples

{
##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"))
}