R/setClasses.R

In SRenan/PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

## =========================================================================##
## =========================================================================## Class definitions and contructors ##
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#' @exportClass ping
setClass("ping", contains = "pics")

#' @exportClass pingError
setClass("pingError", contains = "picsError")

#' @exportClass pingList
setClass("pingList", representation = representation(PE = "logical"), contains = "picsList")

### Constructor
#' @export
newPing <- function(w, mu, delta, sigmaSqF, sigmaSqR, seMu, seMuF, seMuR, score, scoreF, scoreR, Nmerged, converge, range, 
    chr) {
    if (!all(is.double(w))) {
        stop("Argument 'mu' must be numeric ", call. = FALSE)
    }
    if (!all(is.double(mu))) {
        stop("Argument 'mu' must be numeric ", call. = FALSE)
    }
    if (!all(is.double(delta))) {
        stop("Argument 'delta' must be numeric ", call. = FALSE)
    }
    if (!all(is.double(sigmaSqF)) | !all(is.double(sigmaSqR))) {
        stop("Argument 'sigmaSqF/sigmaSqR' must be numeric ", call. = FALSE)
    }
    # if(!all(is.double(seMu)) | !all(is.double(seMuF)) | !all(is.double(seMuR))) { stop('Argument 'seMu/seMuF/seMuR' must
    # be numeric ', call.=FALSE) }
    if (!all(is.double(score))) {
        stop("Argument 'score' must be numeric ", call. = FALSE)
    }
    if (!is.numeric(Nmerged)) {
        stop("Argument 'Nmerged' must be numeric ", call. = FALSE)
    }
    if (!is.logical(converge)) {
        stop("Argument 'converge' must be logical ", call. = FALSE)
    }
    if (!is.character(chr)) {
        stop("Argument 'chr' must be a character string", call. = FALSE)
    }
    # if(!all(is.numeric(range))) { stop('Argument 'range' must be numeric ', call.=FALSE) }
    new("ping", estimates = list(w = w, mu = mu, delta = delta, sigmaSqF = sigmaSqF, sigmaSqR = sigmaSqR, seMu = seMu, 
        seMuF = seMuF, seMuR = seMuR), converge = converge, score = score, scoreF = scoreF, scoreR = scoreR, Nmerged = Nmerged, 
        range = range, chr = chr)
}

# In case the algorithm does not converge
#' @export
newPingError <- function(string) {
    if (!is.character(string)) {
        stop("Argument 'errorCode' must be of class character", call. = FALSE)
    }
    new("pingError", errorCode = string)
}

#' @export
newPingList <- function(List, paraEM, paraPrior, minReads, N, Nc, PE) {
    if (!is.list(paraEM) & !all(sapply(paraEM, "is.numeric"))) {
        stop("Argument 'paraEM' must be a list of numeric arguments", call. = FALSE)
    }
    if (!is.list(paraPrior) & !all(sapply(paraPrior, "is.numeric"))) {
        stop("Argument 'paraPrior' must be a list of numeric arguments", call. = FALSE)
    }
    if (!is.list(minReads) & !all(sapply(minReads, "is.numeric"))) {
        stop("Argument 'minReads' must be a list of numeric arguments", call. = FALSE)
    }
    if (!all((lapply(List, "class") == "ping" | lapply(List, "class") == "pingError"))) {
        stop("Argument 'List' must be a list of 'ping' or 'pingError' arguments", call. = FALSE)
    }
    if (!is.integer(N) | !is.integer(Nc)) {
        stop("Argument 'N' and 'Nc' must be integers", call. = FALSE)
    }
    PE <- as.logical(PE)
    if (!is.logical(PE)) {
        stop("Argument 'PE' must be logical", call. = FALSE)
    }
    new("pingList", List = List, paraEM = paraEM, paraPrior = paraPrior, minReads = minReads, N = N, Nc = Nc, PE = PE)
}