R/GenomicRatioSet-class.R

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

# Exported classes -------------------------------------------------------------

setClass(
    "GenomicRatioSet",
    representation(preprocessMethod = "character", annotation = "character"),
    contains = "RangedSummarizedExperiment")

# Validity methods -------------------------------------------------------------

setValidity("GenomicRatioSet", function(object) {
    msg <- validMsg(NULL, NULL)
    # NOTE: Do not check for the presence of 'CN' because it is optional
    msgBeta <- .checkAssayNames(object, "Beta")
    msgM <- .checkAssayNames(object, "M")
    if (!is.null(msgBeta) && !is.null(msgM)) {
        msg <- validMsg(
            msg,
            sprintf("objects of class '%s needs to have assays slots either 'Beta' or 'M' or both",
                    class(object)))
    }
    if (!is(rowRanges(object), "GRanges")) {
        msg <- validMsg(
            msg,
            sprintf("object of class '%s' needs to have a 'GRanges' in slot 'rowRanges'",
                    class(object)))
    }
    if (is.null(msg)) TRUE else msg
})

# Exported functions -----------------------------------------------------------

GenomicRatioSet <- function(gr = GRanges(), Beta = NULL, M = NULL, CN = NULL,
                            annotation = "", preprocessMethod = "", ...) {
    msg <- "Need either 'Beta' or 'M' or both"
    if (is.null(Beta) && is.null(M)) stop(msg)
    assays <- SimpleList(Beta = Beta, M = M, CN = CN)
    assays <- assays[!vapply(assays, is.null, logical(1L))]
    new("GenomicRatioSet",
        SummarizedExperiment(
            assays = assays,
            rowRanges = as(gr, "GRanges"),
            ...),
        annotation = annotation,
        preprocessMethod = preprocessMethod
    )
}

# Exported methods -------------------------------------------------------------

setMethod("show", signature(object = "GenomicRatioSet"), function(object) {
    callNextMethod()
    .show.annotation(annotation(object))
    .show.preprocessMethod(preprocessMethod(object))
})

setMethod("getBeta", signature(object = "GenomicRatioSet"), function(object) {
    nms <- names(assays(object, withDimnames = FALSE))
    if ("Beta" %in% nms) return(assay(object, "Beta"))
    if ("M" %in% nms) return(ilogit2(assay(object, "M")))
    stop("object does not contain either 'M' nor 'Beta' amongst assay slots")
})

setMethod("getM", signature(object = "GenomicRatioSet"), function(object) {
    nms <- names(assays(object, withDimnames = FALSE))
    if ("M" %in% nms) return(assay(object, "M"))
    if ("Beta" %in% nms) return(logit2(assay(object, "Beta")))
    stop("object does not contain either 'M' nor 'Beta' amongst assay slots")
})

setMethod("getCN", signature(object = "GenomicRatioSet"), function(object) {
    nms <- names(assays(object, withDimnames = FALSE))
    if ("CN" %in% nms) return(assay(object, "CN"))
    NULL
})

setMethod(
    "mapToGenome",
    signature(object = "GenomicRatioSet"),
    function(object, ...) object
)

setMethod(
    "preprocessMethod",
    signature(object = "GenomicRatioSet"),
    function(object) object@preprocessMethod
)

setMethod(
    "annotation",
    signature(object = "GenomicRatioSet"),
    function(object) object@annotation
)

setReplaceMethod(
    "annotation",
    signature(object = "GenomicRatioSet"),
    function(object, value) {
        object@annotation <- value
        object
    }
)

setMethod(
    "updateObject",
    signature(object = "GenomicRatioSet"),
    function(object, ..., verbose = FALSE) {
        if (object@annotation["annotation"] == "ilmn.v1.2") {
            object@annotation["annotation"] <- .default.450k.annotation
        }
        object
    }
)

setMethod(
    "combine",
    signature(x = "GenomicRatioSet", y = "GenomicRatioSet"),
    function(x, y, ...) {
        colDataFix <- .harmonizeDataFrames(.pDataFix(colData(x)),
                                           .pDataFix(colData(y)))
        colData(x) <- colDataFix$x
        colData(y) <- colDataFix$y
        cbind(x,y)
    }
)