R/bindist.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

#' Class \code{"bindist"}
#' 
#' An object of class \code{"bindist"} represents the relevant fixed-width
#' range of binding site from the feature and number of possible binding site
#' in each range.
#' 
#' 
#' @name bindist-class
#' @rdname bindist
#' @aliases bindist bindist-class bindist-method $,bindist-method
#' $<-,bindist-method
#' @docType class
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("bindist", counts="integer", mids="integer",
#' halfBinSize="integer", bindingType="character", featureType="character")}.
#' @seealso \link{preparePool}, \link{peakPermTest}
#' @exportClass bindist
#' @exportMethod "$" "$<-"
#' @keywords classes

setClass("bindist", representation(counts="integer",
                            mids="integer",
                            halfBinSize="integer",
                            bindingType="character",
                            featureType="character"),
         validity=function(object){
             re <- TRUE
             if(is.null(object@counts)) re <- "counts is empty"
             if(is.null(object@mids)) re <- "mids is empty"
             if(is.null(object@halfBinSize)) re <- "halfBinSize is empty"
             if(length(object@halfBinSize)>1) re <- "length of halfBinSize must be 1"
             if(length(object@counts)!=length(object@mids)) 
                 re <- "the length of mids and counts are not identical"
             if(!object@bindingType %in% c("TSS", "geneEnd"))
                 re <- "the bindingType must be TSS or geneEnd"
             if(!object@featureType %in% c("transcript", "exon"))
                 re <- "the featureType must be transcript or exon"
             re
         })

setMethod("$", "bindist", function(x, name) slot(x, name))
setReplaceMethod("$", "bindist",
                 function(x, name, value){
                     slot(x, name, check = TRUE) <- value
                     x
                 })