R/Study.R

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

# ++++++++++++++
# Class: Study 
# ++++++++++++++
#' @include Commons.R 
NULL

#' Class Study 
#'
#' The class contains the functions that handle the data of a specified study.
#'
#' @import methods
#' @slot phsAcc a character string. A dbGaP study accession.
#' @export Study 
#' @import plyr
#' @importFrom reshape2 melt 
#' @import VennDiagram
#' @import futile.logger
#' @import ggplot2
#' @examples 
#' \dontrun{
#'
#' s <- new("Study", phsAcc = 'phs000001.v1.p1')
#' s <- Study(phsAcc = 'phs000001.v1.p1')
#'}

Study <- setClass("Study",
                  slots = list(
                               phsAcc = 'character'
                               ),

                  # Set the default values for the slots
                  prototype = list(
                                   phsAcc = ''
                                   ),

                  validity = function(object) {
                      errors <- character()
                      phsAcc <- object@phsAcc

                      # Validate accession
                      phsAcc <- cleanObjAcc(object, acc = phsAcc, type = 'phs')


                      # Accession format check
                      phsAcc.rex <- "^phs\\d{6}.v\\d+"
                      phsAcc.match <- grepl(phsAcc.rex, object@phsAcc, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)

                  },

                  contains = "Commons"

                  )

# ----------------------
# Method: initialize 
# ----------------------

#' Initialize Study class 
#'
#' The method initializes the Study class. Once the class is initialized, the input study accession and all varibles associated with the parent class Commons become available to all classs methods through the class object. 
#'
#' @param .Object private arugment used in class init 
#' @param ... There are optional arguments. 
#' @param phsAcc a character string. A dbGaP study accession.
#' @examples 
#' \dontrun{
#'
#' s <- new("Study", phsAcc = 'phs000001.v1.p1')
#' s <- Study(phsAcc = 'phs000001.v1.p1')
#'}

#'
setMethod("initialize",
          "Study",
          function(.Object, ..., phsAcc = .Object@phsAcc) {

              .Object <- callNextMethod()

              # Validate accession
              phsAcc <- cleanObjAcc(.Object, acc = phsAcc, type = 'phs')


              .Object@phsAcc <- phsAcc

              msg <- paste("Class Study is initialized with ", phsAcc, ".\n", sep="")
              cat(msg)

              .Object
          })


# ----------------
# Method: show 
# ----------------

#' Display class methods 
#'
#' The method displays all the available methods in the Study class.
#'
#' @param object Study class object. 
#' @export show
#' @examples
#' \dontrun{
#'
#' s <- Study(phsAcc = 'phs000001.v1.p1')
#' show(s) 
#'}
#
setMethod(
          f="show", 
          signature="Study",
          definition=function(object) {
              cat("\n")
              cat("Class Methods:\n")

              # Note: set where=search() to show only S4 method 
              s4Methods <- classMethods <- showMethods(classes="Study", where = search(), showEmpty = FALSE, inherited = TRUE, printTo = FALSE)
              s4MethodsCombo = paste(s4Methods, collapse="\n")
              cat("\n")
              cat(s4MethodsCombo)
              cat("\n")


          })






####################################
# List of functions of this Class 
####################################
# initialize
# show
# getVariableDataByPhvAccAndSubjId 
# getVariableDataByPhvAcc 
# viewStudyVariableInfo 
# getPhvAccListByTerms
# getStudyVariableInfo 
# getVariableInfoByPhvAcc
# getDatasetDataByPhtAcc
# checkObjStudyByAcc
# checkPhvAccList 
# variableDataSummary 
# variableHistogram
# variableScatterplot
# variableBoxplot
# variablePiechart
# variableSubjVenndiagram
# variableCorrelgram