R/classes.R

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

#' Class whippetDataSet
#'
#' Class \code{whippetDataSet} contains information read from whippet output files
#'
#' @name whippetDataSet-class
#' @rdname whippetDataSet-class
#' @exportClass whippetDataSet
#' @import methods
setClass("whippetDataSet", slots = list(
    coordinates = "GRanges",
    diffSplicingResults = "data.frame",
    comparisons = "character",
    junctions = "GRanges",
    readCounts = "data.frame",
    filePath = "character"
))

#' Method diffSplicingResults
#' @name diffSplicingResults
#' @rdname diffSplicingResults-methods
#' @exportMethod diffSplicingResults
#' @import methods
#' @param whippetDataSet whippetDataSet generated from \code{readWhippetDataSet()}
setGeneric("diffSplicingResults",
    def = function(whippetDataSet) {
        standardGeneric("diffSplicingResults")
    }
)

#' @rdname diffSplicingResults-methods
#' @return differential splicing results data.frame
#' (originally from a whippet .diff file)
#' @family whippet data processing
#' @examples
#' whippetFiles <- system.file("extdata", "whippet_small/",
#'     package = "GeneStructureTools"
#' )
#' wds <- readWhippetDataSet(whippetFiles)
#'
#' diffSplicingResults <- diffSplicingResults(wds)
setMethod("diffSplicingResults",
    signature = "whippetDataSet",
    definition = function(whippetDataSet) {
        return(whippetDataSet@diffSplicingResults)
    }
)

#' Method readCounts
#' @name readCounts
#' @rdname readCounts-methods
#' @exportMethod readCounts
#' @import methods
#' @param whippetDataSet whippetDataSet generated from \code{readWhippetDataSet()}
setGeneric("readCounts",
    def = function(whippetDataSet) {
        standardGeneric("readCounts")
    }
)
#' @rdname readCounts-methods
#' @return whippet read count data.frame
#' (originally from a whippet .psi file)
#' @family whippet data processing
#' @examples
#' whippetFiles <- system.file("extdata", "whippet_small/",
#'     package = "GeneStructureTools"
#' )
#' wds <- readWhippetDataSet(whippetFiles)
#'
#' readCounts <- readCounts(wds)
setMethod("readCounts",
    signature = "whippetDataSet",
    definition = function(whippetDataSet) {
        return(whippetDataSet@readCounts)
    }
)

#' Method junctions
#' @name junctions
#' @rdname junctions-methods
#' @exportMethod junctions
#' @import methods
#' @param whippetDataSet whippetDataSet generated from \code{readWhippetDataSet()}
setGeneric("junctions",
    def = function(whippetDataSet) {
        standardGeneric("junctions")
    }
)
#' @rdname junctions-methods
#' @return junctions GRanges object
#' (originally from a whippet .jnc file)
#' @family whippet data processing
#' @examples
#' whippetFiles <- system.file("extdata", "whippet_small/",
#'     package = "GeneStructureTools"
#' )
#' wds <- readWhippetDataSet(whippetFiles)
#'
#' junctions <- junctions(wds)
setMethod("junctions",
    signature = "whippetDataSet",
    definition = function(whippetDataSet) {
        return(whippetDataSet@junctions)
    }
)

#' Method coordinates
#' @name coordinates
#' @rdname coordinates-methods
#' @exportMethod coordinates
#' @param whippetDataSet whippetDataSet generated from \code{readWhippetDataSet()}
setGeneric("coordinates",
    def = function(whippetDataSet) {
        standardGeneric("coordinates")
    }
)
#' @rdname coordinates-methods
#' @return whippet splicing event coordinates as a GRanges object
#' @family whippet data processing
#' @examples
#' whippetFiles <- system.file("extdata", "whippet_small/",
#'     package = "GeneStructureTools"
#' )
#' wds <- readWhippetDataSet(whippetFiles)
#'
#' coordinates <- coordinates(wds)
setMethod("coordinates",
    signature = "whippetDataSet",
    definition = function(whippetDataSet) {
        return(whippetDataSet@coordinates)
    }
)



##' Class rmatsDataSet
#'
#' Class \code{rmatsDataSet} contains information read from rmats output files
#'
#' @name rmatsDataSet-class
#' @rdname rmatsDataSet-class
#' @exportClass rmatsDataSet
#' @import methods
setClass("rmatsDataSet", slots = list(
    SE = "data.frame",
    MXE = "data.frame",
    RI = "data.frame",
    A3SS = "data.frame",
    A5SS = "data.frame",
    filePath = "character"
))

#' Method extractEvent
#' @name extractEvent
#' @rdname extractEvent-methods
#' @exportMethod extractEvent
#' @import methods
#' @param rmatsDataSet rmatsDataSet generated from \code{readRmatsDataSet()}
#' @param eventType specific event type to extract results for.
#' Must be SE/MXE/RI/A5SS/A3SS.
setGeneric("extractEvent",
    def = function(rmatsDataSet, eventType) {
        standardGeneric("extractEvent")
    }
)

#' @rdname extractEvent-methods
#' @return differential splicing results data.frame
#' (originally from a whippet .diff file)
#' @family rmats data processing
#' @examples
#' rmats_directory <- system.file("extdata", "rmats_small/",
#'     package = "GeneStructureTools"
#' )
#' rds <- readRmatsDataSet(rmats_directory)
#' rds.SE <- extractEvent(rds, "SE")
setMethod("extractEvent",
    signature = "rmatsDataSet",
    definition = function(rmatsDataSet, eventType) {
        return(slot(rmatsDataSet, eventType))
    }
)

#' Class irfDataSet
#'
#' Class \code{irfDataSet} contains information read from irf output files
#'
#' @name irfDataSet-class
#' @rdname irfDataSet-class
#' @exportClass irfDataSet
#' @import methods
setClass("irfDataSet", slots = list(
    coordinates = "GRanges",
    IRFresults = "data.frame",
    filePath = "character"
))

#' Method irfResults
#' @name irfResults
#' @rdname irfResults-methods
#' @exportMethod irfResults
#' @import methods
#' @param irfDataSet irfDataSet generated from \code{readIRFDataSet()}
setGeneric("irfResults",
    def = function(irfDataSet) {
        standardGeneric("irfResults")
    }
)

#' @rdname irfResults-methods
#' @return differential splicing results data.frame
#' (originally from a whippet .diff file)
#' @family irf data processing
#' @examples
#' irfinder_file <- list.files(system.file("extdata","irf_small/",
#' package="GeneStructureTools"), full.names=TRUE)
#' irf <- readIrfDataSet(irfinder_file)
#' irf.results <- irfResults(irfDataSet)
setMethod("irfResults",
    signature = "irfDataSet",
    definition = function(irfDataSet) {
        return(slot(irfDataSet, "IRFresults"))
    }
)