R/totalReads-method.R

In DMCHMM: Differentially Methylated CpG using Hidden Markov Model

.totalReads <- function(object) {
    return(assays(object)$totalReads)
}

.replace.totalReads <- function(object, value) {
    assays(object, withDimnames = FALSE)$totalReads <- value
    return(object)
}

#' @rdname totalReads-method
#' @aliases totalReads-method totalReads
setMethod("totalReads", signature(object = "BSData"), .totalReads)

#' @rdname totalReads-method
#' @aliases totalReads-method totalReads<-
setReplaceMethod("totalReads", signature(object = "BSData", value = "matrix"),
    .replace.totalReads)

#' @rdname totalReads-method
#' @aliases totalReads-method totalReads
setMethod("totalReads", signature(object = "BSDMCs"), .totalReads)

#' @rdname totalReads-method
#' @aliases totalReads-method totalReads<-
setReplaceMethod("totalReads", signature(object = "BSDMCs", value = "matrix"),
    .replace.totalReads)