R/GenomicInteractions-class.R

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

## Definition of GenomicInteractions

#' A S4 class to represent interactions between genomic regions.
#'
#'  @slot metadata List, defaults to 'experiment_name' and 'description', inherited from S4Vectors::Vector
#'  @slot anchor_one,anchor_two GRanges. Set of anchors of interactions.
#'  @slot counts integer vector, contains raw counts
#'  @slot elementMetadata DataFrame
#'  
#' This class is used to store information on which genomic regions are
#' interacting with each other. Objects of this class contain information of
#' the genomic coordinates of the interacting regions and the strength of these
#' interactions, and associated metadata such as the name of the dataset and a
#' brief description of the dataset.  Interacting regions are stored as a pair
#' of GenomicRanges: each set of anchor regions is stored as a separate
#' GenomicRanges object, accessed by \code{getAnchorOne} and
#' \code{getAnchorTwo}.
#'
#' @examples
#'
#' showClass('GenomicInteractions')
#' 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)
#'
#' @import GenomicRanges
#' @importFrom S4Vectors DataFrame setValidity2
#' @import InteractionSet
#' @import methods
#'
#' @exportClass GenomicInteractions

setClass("GenomicInteractions", contains = "GInteractions", representation(anchor1 = "integer", anchor2 = "integer", regions = "GRanges", 
    NAMES = "character_OR_NULL"), prototype(anchor1 = integer(0), anchor2 = integer(0), regions = GRanges(), elementMetadata = DataFrame(counts = integer(0)), 
    NAMES = NULL))

setValidity2("GenomicInteractions", function(object) {
    if (!("counts" %in% names(object@elementMetadata))) {
        stop("Valid GenomicInteractions object must contain counts")
    }
    if (!is.integer(object@elementMetadata$counts) || !(all(is.finite(object@elementMetadata$counts))) || !all(object@elementMetadata$counts >= 
        0)) {
        stop("'counts' must be finite positive integers")
    }
    return(TRUE)
})


#' Function to create a GenomicInteractions object
#'
#' Create GenomicInteractions objects from two GRanges ojects.
#'
#' @param anchor1,anchor2 GRanges objects.
#' @param counts An integer vector, defaults to 1.
#' @param ... Additional data to be added to mcols
#' @return a GenomicInteractions object
#' @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)
#'
#' @export
setGeneric("GenomicInteractions", function(anchor1, anchor2, counts, ...) {
    standardGeneric("GenomicInteractions")
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("GRanges", "GRanges", "numeric"), function(anchor1, anchor2, counts, ...) {
    out <- GInteractions(anchor1, anchor2, counts = counts, ...)
    class(out) <- "GenomicInteractions"
    out
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("GInteractions"), function(anchor1) {
    out <- anchor1
    
    if (!("counts" %in% names(out@elementMetadata))) {
        out@elementMetadata$counts <- rep(as.integer(1), length(out))
    } else {
        out@elementMetadata$counts <- as.integer(out@elementMetadata$counts)
    }
    class(out) <- "GenomicInteractions"
    out
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("GInteractions", "numeric"), function(anchor1, anchor2) {
    out <- anchor1
    out$counts <- as.integer(anchor2)
    class(out) <- "GenomicInteractions"
    out
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("numeric", "numeric", "GRanges"), function(anchor1, anchor2, counts, ...) {
    GenomicInteractions(GInteractions(anchor1, anchor2, counts, ...))
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("GRanges", "GRanges", "GenomicRanges_OR_missing"), function(anchor1, anchor2, counts, ...) {
    if (missing(counts)) {
        GenomicInteractions(GInteractions(anchor1, anchor2, ...))
    } else {
        GenomicInteractions(GInteractions(anchor1, anchor2, counts, ...))
    }
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("missing", "missing", "GenomicRanges_OR_missing"), function(anchor1, anchor2, counts, ...) {
    if (missing(counts)) {
        GenomicInteractions(GInteractions())
    } else {
        GenomicInteractions(GInteractions(integer(0), integer(0), counts))
    }
})

#' @rdname GenomicInteractions
setMethod("GenomicInteractions", c("ANY", "ANY", "ANY"), function(anchor1, anchor2, counts, ...) {
    GenomicInteractions(GInteractions(anchor1, anchor2, counts, ...))
})

############################################################################### 
#' updateObject method for GenomicInteractions 1.3.7 and earlier
#' 
#' @inheritParams BiocGenerics::updateObject
#' @return A GenomicInteractions object
#' @importFrom Biobase updateObject
#' @importFrom BiocGenerics getObjectSlots
#' @export

setMethod("updateObject", signature(object = "GenomicInteractions"), function(object, ..., verbose = FALSE) {
    if (verbose) {
        message("updating GenomicInteractions object")
    }
    
    if ("anchor_one" %in% names(getObjectSlots(object))) {
        anchor1 <- object@anchor_one
        anchor2 <- object@anchor_two
        all_anchors <- unique(c(object@anchor_one, object@anchor_two))
        mcols(anchor1) <- NULL
        mcols(anchor2) <- NULL
        
        em <- DataFrame(counts = object@counts, object@elementMetadata)
        
        newobj <- GInteractions(anchor1, anchor2, all_anchors, metadata = object@metadata, elementMetadata = em)
        
        class(newobj) <- "GenomicInteractions"
        names(mcols(newobj)) <- gsub("elementMetadata.", "", names(mcols(newobj)))
        newobj
    } else {
        object
    }
})