R/DAVIDGeneCluster-class.R

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

#' class "DAVIDGeneCluster" 
#'
#' This class represents the output of a DAVID Gene Functional Classification
#' Tool report.
#'
#' @section Type:
#' This class is a "\code{Concrete}" one.
#'
#' @section Extends:
#' \itemize{
#'  \item \emph{DAVIDCluster} and uses its constructor to parse the report.
#' }
#'
#' @section Slots: the ones inherited from DAVIDCluster.
#'
#' @section Methods:
#' \describe{
#' \item{\code{initialize}}{\code{signature(.Object="DAVIDGeneCluster",
#' fileName="character")}: basic cluster report file parser.}
#' \item{\code{DAVIDGeneCluster}}{\code{signature(fileName="character")}:
#' high level gene cluster report file parser.}
#' \item{\code{ids}}{\code{signature(object="DAVIDGeneCluster")}: list
#' with the member ids within each cluster.}
#' \item{\code{genes}}{\code{signature(object="DAVIDGeneCluster")}: list
#' with the DAVIDGenes members within each cluster.}
#' \item{\code{plot2D}}{\code{signature(object="DAVIDGeneCluster", 
#' color=c("FALSE"="black","TRUE"="green"), names=FALSE)}: ggplot2 tile plot
#' with gene membership to each cluster.}
#' }
#'
#' @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 DAVIDGeneCluster
#' @name DAVIDGeneCluster-class
#' @rdname DAVIDGeneCluster-class
#' @exportClass DAVIDGeneCluster
#' @examples
#' {
#' ##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)))
#' }
#' 
setClass(Class="DAVIDGeneCluster", contains="DAVIDCluster", 
  prototype=prototype(type="GeneCluster"))