R/loadFromFiles.R

In methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

#' Load \pkg{methimpute} objects from file
#'
#' Wrapper to load \pkg{\link{methimpute}} objects from file and check the class of the loaded objects.
#'
#' @param files A list of \code{\link{GRanges-class}} or \code{\link{methimputeBinomialHMM}} objects or a character vector with files that contain such objects.
#' @param check.class Any combination of \code{c('GRanges', 'methimputeBinomialHMM')}. If any of the loaded objects does not belong to the specified class, an error is thrown.
#' @return A list of \code{\link{GRanges-class}} or \code{\link{methimputeBinomialHMM}} objects.
#' 
#' @export
#' @examples
#'## Get some files that you want to load
#'file <- system.file("data","arabidopsis_toydata.RData",
#'                     package="methimpute")
#'## Load and print
#'data <- loadFromFiles(file)
#'print(data)
#'
loadFromFiles <- function(files, check.class=c('GRanges','methimputeBinomialHMM')) {

    available.classes <- c('GRanges', 'methimputeBinomialHMM')
    # ptm <- startTimedMessage("Loading data from files ...")
    if (is.null(files)) {
        # stopTimedMessage(ptm)
        return(files)
    }
    if (any(! check.class %in% available.classes)) {
        stop("Argument 'check.class' must contain any combination of c('", paste0(available.classes, collapse="', '"), "').")
    }
    modellist <- list()
    if (is.character(files)) {
        for (file in files) {
            temp.env <- new.env()
            model <- get(load(file, envir=temp.env), envir=temp.env)
            if (! class(model) %in% check.class) {
                stop("File '", file, "' does not contain an object of class ", paste0(check.class, collapse=' or '), ".")
            }
            modellist[[file]] <- model
        }
        if (!is.null(names(files))) {
            names(modellist) <- names(files)
        }
    } else if (class(files) %in% check.class) {
        modellist[[1]] <- files
    } else if (is.list(files)) {
        for (file in files) {
            model <- file
            if (! class(model) %in% check.class) {
                stop("List entry '", length(modellist)+1, "' does not contain an object of class ", paste0(check.class, collapse=' or '), ".")
            }
            modellist[[length(modellist)+1]] <- model
        }
        names(modellist) <- names(files)
    } else if (! class(files) %in% check.class) {
        stop("Input does not contain an object of class ", paste0(check.class, collapse=' or '), ".")
    }
    # stopTimedMessage(ptm)
    return(modellist)

}