R/setters.R

In ComputationalRegulatoryGenomicsICL/GenomicInteractions-new: Utilities for handling genomic interaction data

#' Functions to set data held in a GInteractions object.
#'
#' Use these functions to set data stored in each of the slots of a
#' GInteractions object.
#'
#' @name setters
#' @param GIObject A GenomicInteractions object
#' @param value A vector to replace a slot in the object
#' @return GenomicInteractions object
#' @rdname setters
#' @examples
#'
#' library(GenomicRanges)
#'
#' anchor.one = GRanges(c('chr1', 'chr1', 'chr1', 'chr1'), IRanges(c(10, 20, 30, 20), width=5))
#' anchor.two = GRanges(c('chr1', 'chr1', 'chr1', 'chr2'), IRanges(c(100, 200, 300, 50), width=5))
#' interaction_counts = sample(1:10, 4)
#' test <- GenomicInteractions(anchor.one, anchor.two, experiment_name='test', 
#'                            description='this is a test', counts=interaction_counts)
#'
#' name(test) <- 'Mouse test'
#' name(test)
#'
#' description(test) <- 'This is a test using the mouse genome'
#' description(test)
#'
#' interactionCounts(test) <- c(2,3,8,5)
#' interactionCounts(test)
#'
## GENERICS
#' @rdname setters
#' @aliases name<-
#' @export
setGeneric("name<-", function(GIObject, value) {
    standardGeneric("name<-")
})

#' @rdname setters
#' @export
setGeneric("interactionCounts<-", function(GIObject, value) {
    standardGeneric("interactionCounts<-")
})

## METHODS

#' @rdname setters
#' @export
setReplaceMethod("name", "GInteractions", function(GIObject, value) {
    GIObject@metadata$experiment_name <- value
    GIObject
})

#' @rdname setters
#' @inheritParams Biobase::'description<-'
#' @importMethodsFrom Biobase 'description<-'
#' @export
setReplaceMethod("description", "GInteractions", function(object, value) {
    object@metadata$description <- value
    object
})

#' @rdname setters
#' @export
setReplaceMethod("interactionCounts", "GInteractions", function(GIObject, value) {
    if (!all(value == floor(value))) 
        stop("value must contain integer values")
    value <- as.integer(value)
    if (length(value) == 1) 
        value <- rep(value, length(GIObject))
    GIObject@elementMetadata$counts <- value
    GIObject
})