R/DAVIDCluster-class.R

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

#' class "DAVIDCluster"
#'
#' This virtual class represents the output of a DAVID "Cluster" report, with
#' "DAVIDTermCluster" and "DAVIDGeneCluster" as possible heirs, according to
#' the report used.
#'
#' @section Type:
#' This class is a "\code{Virtual}" one.
#'
#' @section Extends:
#' \itemize{
#'  \item \emph{DAVIDResult} in the conceptual way.
#' }
#'
#' @section Heirs:
#' \itemize{
#'  \item \code{DAVIDTermCluster}: DAVID's Functional Annotation Clustering
#'  report.
#'  \item \code{DAVIDGeneCluster}: DAVID's Functional Classification Tool
#'  report.
#' }
#'
#' @section Slots:
#' \describe{
#'  \item{\code{cluster}}{named list with the different clustered terms/genes:
#'  Members, represented as DAVIDGenes object; and EnrichmentScore, a numeric
#'  with DAVID cluster enrichment score.}
#' }
#'
#' @section Methods:
#' \describe{
#' \item{\code{show}}{\code{signature(object="DAVIDCluster")}: basic
#'  console output.}
#' \item{\code{summary}}{\code{signature(object="DAVIDCluster")}: basic
#'  summary console output.}
#' \item{\code{initialize}}{\code{signature(object="DAVIDCluster",
#' fileName="character")}: basic cluster report file parser.}
#' \item{\code{cluster}}{\code{signature(object="DAVIDCluster")}: getter
#' for the corresponding slot.}
#' \item{\code{enrichment}}{\code{signature(object="DAVIDCluster")}: obtain the
#' enrichment score of each cluster.}
#' \item{\code{members}}{\code{signature(object="DAVIDCluster")}: obtain
#' the corresponding cluster members.}
#' }
#'
#' @author Cristobal Fresno and Elmer A Fernandez
#' 
#' @references 
#' \enumerate{
#'  \item The Database for Annotation, Visualization and Integrated Discovery 
#'  (david.abcc.ncifcrf.gov)
#'  \item 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
#' }
#'
#' @docType class
#' @keywords classes 
#' @family DAVIDCluster
#' @name DAVIDCluster-class
#' @rdname DAVIDCluster-class
#' @exportClass DAVIDCluster
setClass(Class="DAVIDCluster",
  representation=representation(cluster="list", "VIRTUAL"),
  contains="DAVIDResult",
  prototype=prototype(type="generic cluster", cluster=list())
)