R/calculateDistances.R

In ComputationalRegulatoryGenomicsICL/GenomicInteractions: Utilities for handling genomic interaction data

#' Calculate interaction distances
#'
#' This function takes a GInteractions object and calculates the distances
#' between the anchors according to the value of \code{method}. The distances
#' returned follow the same convention as distance(x, y) in GenomicRanges where
#' the distance between adjacent regions is 0. Note that if anchors are
#' overlapping this method will print a warning and return the distance as 0.
#'
#' @param GIObject A GInteractions object
#' @param method Character vector indicating how to calculate distances, must be
#'   one of `midpoint', `outer', `inner'.
#' @param floor A logical specifying whether to round down distances to nearest
#'   base pair or not. Default TRUE.
#'
#' @return An vector containing the distances between anchors/GRanges, NA if on
#'   different chromosomes, rounded down to the nearest bp.
#' @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)
#' calculateDistances(test, method = 'midpoint')
#'
#' @docType methods
#' @rdname calculateDistances
#' @export
setGeneric("calculateDistances", function(GIObject, method = "midpoint", floor = TRUE) {
    standardGeneric("calculateDistances")
})

#' @rdname calculateDistances
#' @export
setMethod("calculateDistances", c("GInteractions"), function(GIObject, method = "midpoint", floor = TRUE) {
    if (method == "midpoint") {
        distances <- pairdist(GIObject, type = "mid")
    } else if (method == "outer") {
        distances <- pairdist(GIObject, type = "span")
    } else if (method == "inner") {
        distances <- pairdist(GIObject, type = "gap")
    } else {
        distances <- pairdist(GIObject, type = method)
    }
    
    if (floor) {
        return(floor(distances))
    } else {
        return(distances)
    }
})


setGeneric(".calculateDistances.df", function(object1, object2, method = "midpoint", floor = TRUE) {
    standardGeneric(".calculateDistances.df")
})

setMethod(".calculateDistances.df", c("data.frame", "data.frame"), function(object1, object2, method = "midpoint", floor = TRUE) {
    if (method == "midpoint") {
        midpt.one <- (object1$start + object1$end)/2
        midpt.two <- (object2$start + object2$end)/2
        distances <- ifelse(object1$seqnames == object2$seqnames, ifelse(midpt.two > midpt.one, midpt.two - midpt.one, midpt.one - midpt.two), 
            NA)
    } else if (method == "outer") {
        distances <- ifelse(object1$seqnames == object2$seqnames, ifelse(object2$start > object1$start, object2$end - object1$start + 
            1, object1$end - object2$start + 1), NA)
    } else if (method == "inner") {
        distances <- ifelse(object1$seqnames == object2$seqnames, ifelse(object2$start > object1$start, object2$start - object1$end - 
            1, object1$start - object2$end - 1), NA)
    } else {
        stop("method must be one of c(\"midpoint\", \"outer\", \"inner\")")
    }
    if (floor) {
        return(floor(distances))
    } else {
        return(distances)
    }
})