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