R/getters.R

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

#' Functions to access data held in a GenomicInteractions object.
#'
#' Use these functions to access data stored in each of the slots of a
#' GenomicInteractions object.
#'
#' @name getters
#' @param GIObject A Gnteractions object
#' @rdname getters
#' 
#' @return For 'anchorOne' and 'anchorTwo', a GRanges. For 'interactionCounts', 
#' a numeric vector with counts for each interaction in the object. For
#'   'description' and 'name',  a character vector with
#'   length 1. For 'annotationFeatures', a character vector of features with
#'   which the object was previously annotated, or 'NA' if the object is unannotated.
#'
#' @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, counts=interaction_counts)
#'
#' name(test)
#' description(test)
#' anchorOne(test)
#' anchorTwo(test)
#' interactionCounts(test)

## GENERICS

#' @rdname getters
#' @export
setGeneric("name", function(GIObject) {
    standardGeneric("name")
})

#' @rdname getters
#' @export
setGeneric("anchorOne", function(GIObject) {
    standardGeneric("anchorOne")
})

#' @rdname getters
#' @export
setGeneric("anchorTwo", function(GIObject) {
    standardGeneric("anchorTwo")
})

#' @rdname getters
#' @export
setGeneric("interactionCounts", function(GIObject) {
    standardGeneric("interactionCounts")
})

#' @rdname getters
#' @export
setGeneric("annotationFeatures", function(GIObject) {
    standardGeneric("annotationFeatures")
})

## METHODS

#' @rdname getters
#' @export
#' @aliases name
setMethod("name", "GInteractions", function(GIObject) {
    return(GIObject@metadata$experiment_name)
})

#' @rdname getters
#' @inheritParams Biobase::description
#' @importMethodsFrom Biobase description
#' @export
setMethod("description", c("GInteractions"), function(object) {
    return(object@metadata$description)
})

#' @rdname getters
#' @export
setMethod("anchorOne", "GInteractions", function(GIObject) {
    return(anchors(GIObject, type = "first"))
})

#' @rdname getters
#' @export
setMethod("anchorTwo", "GInteractions", function(GIObject) {
    return(anchors(GIObject, type = "second"))
})

## N.B. this may not apply to all GInteractions objects
#' @rdname getters
#' @export
setMethod("interactionCounts", "GInteractions", function(GIObject) {
    if (!"counts" %in% names(elementMetadata(GIObject))) {
        warning("'counts' not in mcols of object; will return NULL")
    }
    return(GIObject@elementMetadata$counts)
})

#' @rdname getters
#' @export
setMethod("annotationFeatures", "GInteractions", function(GIObject) {
    if ("node.class" %in% names(elementMetadata(GIObject@regions))) {
        annotation <- unique(GIObject@regions$node.class)
    } else {
        annotation <- NA_character_
    }
    return(annotation)
})