R/ioHelpers.R

In rhondabacher/methylscaper: Visualization of Methylation Data

#' This is an internal function for now and a place-holder
#' in case SingleCellExperiment may be
#' used in the future. We may need to update this later. Assumes
#' rownames are formatted like chr_pos and there are two assays.
#' The assay names are `methylation_met` for endogenous methylation
#' and `methylation_acc` for accessibility.
#' @param dataIn Input SCE object passed to the prepSC() function.
#' @return List object containing the met and acc tables.
#' @importFrom SummarizedExperiment assay
reformatSCE <- function(dataIn) {
    check_package("SingleCellExperiment")
    check_package("SummarizedExperiment")

    dataOut.gch <- assay(dataIn, "methylation_acc")
    locs_list <- rownames(dataOut.gch)
    locs_list <- data.frame(do.call(rbind, strsplit(locs_list, "_")))
    colnames(locs_list) <- c("chr", "pos")
    locs_list$pos <- as.numeric(locs_list$pos)
    dataOut.gch.list <- split(dataOut.gch, rep(seq(1, ncol(dataOut.gch)), each = nrow(dataOut.gch)))


    dataOut.hcg <- assay(dataIn, "methylation_met")
    locs_list <- rownames(dataOut.hcg)
    locs_list <- data.frame(do.call(rbind, strsplit(locs_list, "_")))
    colnames(locs_list) <- c("chr", "pos")
    locs_list$pos <- as.numeric(locs_list$pos)
    dataOut.hcg.list <- split(dataOut.hcg, rep(seq(1, ncol(dataOut.hcg)), each = nrow(dataOut.hcg)))
    # dataOut.hcg.list <- lapply(dataOut.hcg.list, function(x) GRanges(seqnames = locs_list$chr,
    #                                         ranges = IRanges(start = locs_list$pos, width = 1L),
    #                                         rate=x))

    return(list(gch = dataOut.gch.list, hcg = dataOut.hcg.list))
}


#' Check if a package is installed
#' @param package Name of the package.
#' @return Message is returned if package not installed.
check_package <- function(package) {
    suppressMessages({
        if (!requireNamespace(package, quietly = TRUE)) {
            stop(package, " package is needed, please install it.")
        }
    })
}