R/methrix_object.R

In methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

#' Class methrix
#' @description S4 class Methrix
#' @slot assays A list of tw omatrices containing 'Methylation' and 'Coverage' information
#' @slot elementMetadata A DataFrame describing rows in correspoding assay matrices.
#' @slot colData genome: the name of the BSgenome that was used to extract CpGs, isHDF5: is it stored in HDF5 Array format
#' @slot metadata a list of meta data associated with the assays
#' @slot NAMES NULL
#' @exportClass methrix
#' @importFrom graphics axis legend lines mtext par plot title
#' @importFrom stats complete.cases cov density median prcomp quantile sd
#' @importFrom utils browseURL
#' @importClassesFrom SummarizedExperiment SummarizedExperiment
#'
methrix <- setClass(Class = "methrix", contains = "SummarizedExperiment")

setMethod(f = "show", signature = "methrix", definition = function(object) {
    cat(paste0("An object of class ", class(object), "\n"))
    cat(paste0("   n_CpGs: ", format(nrow(object), big.mark = ","), "\n"))
    cat(paste0("n_samples: ", ncol(object), "\n"))
    cat(paste0("    is_h5: ", is_h5(object), "\n"))
    cat(paste0("Reference: ", object@metadata$genome, "\n"))
})

# Create methrix obj
create_methrix <- function(beta_mat = NULL, cov_mat = NULL, cpg_loci = NULL,
    is_hdf5 = FALSE, genome_name = "hg19", col_data = NULL, h5_dir = NULL,
    ref_cpg_dt = NULL, chrom_sizes = NULL, desc = NULL) {

    if (is_hdf5) {
        se <- SummarizedExperiment::SummarizedExperiment(assays = list(beta = as(beta_mat,
            "HDF5Array"), cov = as(cov_mat, "HDF5Array")), metadata = list(genome = genome_name,
            is_h5 = is_hdf5, ref_CpG = ref_cpg_dt, chrom_sizes = chrom_sizes,
            descriptive_stats = desc), colData = col_data, rowData = cpg_loci)
        if (!is.null(h5_dir)) {
            tryCatch(HDF5Array::saveHDF5SummarizedExperiment(x = se, dir = h5_dir,
                replace = TRUE), error = function(e)
                    message("The dataset is not saved. Please save manually, using the HDF5Array::saveSummarizedExperiment command. "))
        }
    } else {
        se <- SummarizedExperiment::SummarizedExperiment(assays = list(beta = as.matrix(beta_mat),
            cov = as.matrix(cov_mat)), metadata = list(genome = genome_name,
            is_h5 = is_hdf5, ref_CpG = ref_cpg_dt, chrom_sizes = chrom_sizes,
            descriptive_stats = desc), colData = col_data, rowData = cpg_loci)
    }

    return(methrix(se))
}