R/AllClasses.R

In shokoohi/DMCFB: Differentially Methylated Cytosines via a Bayesian Functional Approach

#' @title params
#' @description parameters name and their descriptions
#' @author Farhad Shokoohi <shokoohi@icloud.com>
#' @name params
#' @param methReads The matrix \code{methReads} contains the number of
#' methylated reads spanning a CpG-site. The rows represent the CpG sites in
#' \code{rowRanges} and the columns represent the samples in \code{colData}.
#' @param totalReads The matrix \code{totalReads} contains the number of reads
#' spanning a CpG-site. The rows represent the CpG sites in \code{rowRanges}
#' and the columns represent the samples in \code{colData}.
#' @param methLevels The matrix \code{methLevels} contains the predicted
#' methylation level spanning a CpG-site using Bayesian functional regression
#' models. The rows represent the CpG sites in \code{rowRanges} and the columns
#' represent the samples in \code{colData}.
#' @param rowRanges A \code{\link{GRanges}} or \code{\link{GRangesList}}
#' object describing the ranges of interest. Names, if present, become the row
#' names of the \code{\link{SummarizedExperiment}} object. The length of the
#' \code{\link{GRanges}} or \code{\link{GRangesList}} must equal the number of
#' rows of the matrices in \code{assays}. If \code{rowRanges} is missing, a
#' \code{\link{SummarizedExperiment}} instance is returned.
#' @param colData Object of class \code{'DataFrame'} containing information on
#' variable values of the samples
#' @param metadata A \code{list} of storing MCMC samples or DMCs
#' @param object A \code{\link{BSDMC-class}}
#' object
#' @param value An integer matrix
#' @param name A character list
#' @param obj1 A \code{\link{BSDMC-class}}
#' @param obj2 A \code{\link{BSDMC-class}}
#' @param files A character list
#' @param file A character
#' @param nCores An integer value specifying the number of machine cores for
#' parallel computing
#' @param mc.cores An integer greater than 0
#' @param pSize An integer value specifying the number of cytosines in a regrion
#' to be used in a Bayesian functiona regression model for DMC detection
#' @param bwa An integer value specifying the band-width size of B-spline basis
#' matrix for a natural cubic spline for the group-specific effects of the
#' Bayesian functional regression model
#' @param bwb An integer value specifying the band-width size of B-spline basis
#' matrix for a natural cubic spline for the individual-specific effects of the
#' Bayesian functional regression model
#' @param nBurn An integer value specifying the number of burn-in samples
#' @param nThin An integer value specifying the thining number in MCMC
#' @param nMC An integer value specifying the number of MCMC samples after
#' burn-in
#' @param sdv An double value specifying the standard deviation of priors
#' @param alpha A numeric value specifying the level of \eqn{\alpha} in credible
#' interval \eqn{(1-\alpha)\%}
#' @param col A character vector indicating which colors to alternate.
#' @param sfiles A logical value indicating whether files to be saved or not.
#' @param region An integer vector of length two specifying which subset of the
#' object to be plotted
#' @param nSplit A integer value specifying the number of subsets must be done
#' for plotting the results of DMC identification
#' @param parList A list specifying plots parameters, see \code{\link{par}}
#' @param ... other possible parameters
#' @docType NULL
NULL

#' @title BSDMC object
#' @description The \code{BSDMC} object is an S4 class that represents
#' differentially methylated CpG sites (DMCs) in BS-Seq Data.
#' @author Farhad Shokoohi <shokoohi@icloud.com>
#' @name BSDMC-class
#' @import methods
#' @import SummarizedExperiment
#' @slot methReads An integer matrix
#' @slot totalReads An integer matrix
#' @slot methLevels A numeric matrix
#' @param methReads The matrix \code{methReads} contains the number of
#' methylated reads spanning a CpG-site. The rows represent the CpG sites in
#' \code{rowRanges} and the columns represent the samples in \code{colData}.
#' @param totalReads The matrix \code{totalReads} contains the number of reads
#' spanning a CpG-site. The rows represent the CpG sites in \code{rowRanges}
#' and the columns represent the samples in \code{colData}.
#' @param methLevels The matrix \code{methLevels} contains the predicted
#' methylation level spanning a CpG-site using Bayesian functional regression
#' models. The rows represent the CpG sites in \code{rowRanges} and the columns
#' represent the samples in \code{colData}.
#' @docType class
#' @keywords object
#' @return A \code{\link{BSDMC-class}} object
#' @seealso \code{\link{RangedSummarizedExperiment-class}}
#' \code{\link{GRanges-class}}
#' @examples
#' nr <- 500
#' nc <- 16
#' metht <- matrix(as.integer(runif(nr * nc, 0, nr)), nr)
#' methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
#' meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
#' methl <- methc / metht
#' methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
#' r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
#' names(r1) <- 1:nr
#' cd1 <- DataFrame(Group = rep(c("G1", "G2"), each = nc / 2),
#'   row.names = LETTERS[1:nc])
#' OBJ2 <- cBSDMC(
#'   rowRanges = r1, methReads = methc, totalReads = metht,
#'   methLevels = methl, methStates = meths, methVars = methv, colData = cd1
#' )
#' OBJ2
#' @exportClass BSDMC
BSDMC <- setClass("BSDMC", representation(
    methReads = "matrix",
    totalReads = "matrix", methLevels = "matrix"
),
prototype(
    methReads = matrix(), totalReads = matrix(),
    methLevels = matrix()
),
contains = "RangedSummarizedExperiment"
)

setValidity("BSDMC", function(object) {
    if (length(assays(object)) != 3) {
    return("The assays slot in BSDMC object must be of length three.")
    }else{
    return(TRUE)
    }
    if (!(all(is.element(assayNames(object), c(
    "methReads", "totalReads",
    "methLevels"
    ))))) {
    return("The assays slot in BSDMC object must contain totalReads,
        methReads and methStates.")
    }else{
    return(TRUE)
    }
    if (!all(vapply(assays(object), class, character(1)) == "matrix")) {
    return("The methReads, totalReads and methLevels slots
        of a BSDMC object must be matrices.")
    }else{
    return(TRUE)
    }
    if (!all(vapply(assays(object), typeof, character(1)) == c(
    "integer",
    "integer", "double"
    ))) {
    return("The methReads, totalReads and methLevels slots
        of a BSDMC object must be integer, integer and double,
        repectively.")
    }else{
    return(TRUE)
    }
})