R/helpers.R

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

# generic definitions of functions defined in this file
#' @rdname InteractionHelpers
#' @export
setGeneric("is.pp", function(GIObject) {
    standardGeneric("is.pp")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.pd", function(GIObject) {
    standardGeneric("is.pd")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.pt", function(GIObject) {
    standardGeneric("is.pt")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.dd", function(GIObject) {
    standardGeneric("is.dd")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.dt", function(GIObject) {
    standardGeneric("is.dt")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.tt", function(GIObject) {
    standardGeneric("is.tt")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("isInteractionType", function(GIObject, x, y) {
    standardGeneric("isInteractionType")
})

#' @rdname InteractionHelpers
#' @param x,y Names of annotated node classes
#' @export
setGeneric("is.trans", function(GIObject) {
    standardGeneric("is.trans")
})

#' @rdname InteractionHelpers
#' @export
setGeneric("is.cis", function(GIObject) {
    standardGeneric("is.cis")
})

#' Interaction Type Helpers
#'
#' Functions to classify interactions within GInteractions objects.
#' \itemize{
#'     \item 'isInteractionType' takes two character arguments which are
#'           annotated node classes and returns interactions between them.
#'     \item 'is.pp', 'is.pd' etc. are bindings for common annotations:
#'     \describe{ \item{p}{promoter}
#'                \item{d}{distal}
#'                \item{t}{terminator} }
#'     \item 'is.trans' & 'is.cis' select trans-chromosomal and
#'           intra-chromosomal interactions, respectively }
#' @param GIObject A GInteractions object
#' @return A logical vector
#' @examples 
#' data(hic_example_data)
#' table(is.cis(hic_example_data))
#' sum(interactionCounts(hic_example_data))
#' 
#' @name InteractionHelpers
#' @rdname InteractionHelpers
NULL

#' @rdname InteractionHelpers
#' @export
setMethod("is.pp", "GInteractions", function(GIObject) {
    return(GIObject@regions$node.class[GIObject@anchor1] == "promoter" & GIObject@regions$node.class[GIObject@anchor2] == "promoter")
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.pd", "GInteractions", function(GIObject) {
    return((GIObject@regions$node.class[GIObject@anchor1] == "distal" & GIObject@regions$node.class[GIObject@anchor2] == "promoter") | 
        (GIObject@regions$node.class[GIObject@anchor1] == "promoter" & GIObject@regions$node.class[GIObject@anchor2] == "distal"))
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.pt", "GInteractions", function(GIObject) {
    return((GIObject@regions$node.class[GIObject@anchor1] == "terminator" & GIObject@regions$node.class[GIObject@anchor2] == "promoter") | 
        (GIObject@regions$node.class[GIObject@anchor1] == "promoter" & GIObject@regions$node.class[GIObject@anchor2] == "terminator"))
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.dd", "GInteractions", function(GIObject) {
    return(GIObject@regions$node.class[GIObject@anchor1] == "distal" & GIObject@regions$node.class[GIObject@anchor2] == "distal")
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.dt", "GInteractions", function(GIObject) {
    return((GIObject@regions$node.class[GIObject@anchor1] == "distal" & GIObject@regions$node.class[GIObject@anchor2] == "terminator") | 
        (GIObject@regions$node.class[GIObject@anchor1] == "terminator" & GIObject@regions$node.class[GIObject@anchor2] == "distal"))
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.tt", "GInteractions", function(GIObject) {
    return(GIObject@regions$node.class[GIObject@anchor1] == "terminator" & GIObject@regions$node.class[GIObject@anchor2] == "terminator")
})

#' @rdname InteractionHelpers
#' @export
setMethod("isInteractionType", "GInteractions", function(GIObject, x, y) {
    return((GIObject@regions$node.class[GIObject@anchor1] %in% x & GIObject@regions$node.class[GIObject@anchor2] %in% y) | (GIObject@regions$node.class[GIObject@anchor1] %in% 
        y & GIObject@regions$node.class[GIObject@anchor2] %in% x))
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.trans", "GInteractions", function(GIObject) {
    return(as.character(seqnames(GIObject@regions[GIObject@anchor1])) != as.character(seqnames(GIObject@regions[GIObject@anchor2])))
})

#' @rdname InteractionHelpers
#' @export
setMethod("is.cis", "GInteractions", function(GIObject) {
    return(as.character(seqnames(GIObject@regions[GIObject@anchor1])) == as.character(seqnames(GIObject@regions[GIObject@anchor2])))
})

#' Return the total number of interactions in a GInteractions GIObject
#'
#' @param x GInteractions GIObject
#' @return The sum of the counts in GIObject
#' @docType methods
#' @export
setMethod("sum", "GInteractions", function(x) {
    return(sum(interactionCounts(x)))
})