R/runMetrics.R

In navinlabcode/copykit: CopyKit

#' Run metrics
#'
#' Calculates the overdispersion and the breakpoint counts for each cell.
#'
#' @author Darlan Conterno Minussi
#'
#' @param scCNA scCNA object.
#' @param BPPARAM A \linkS4class{BiocParallelParam} specifying how the function
#' should be parallelized.
#'
#' @details Adds the metrics to the scCNA \code{\link[SummarizedExperiment]{colData}}.
#'  Those metrics can be used for subsetting the data if desired.
#'  results can be visualized with \code{\link{plotMetrics}}.
#'
#' @return Adds columns 'overdispersion' and 'breakpoint_count' to
#'  \code{\link[SummarizedExperiment]{colData}}.
#'
#' @export
#' @import ggplot2
#'
#' @examples
#' copykit_obj <- mock_bincounts()
#' copykit_obj <- runMetrics(copykit_obj)
runMetrics <- function(scCNA,
                       BPPARAM = bpparam()) {

    ###################
    # Retrieving data

    dat_seg <- segment_ratios(scCNA)
    dat_rat <- ratios(scCNA)
    dat_bin <- bincounts(scCNA)
    rg <- SummarizedExperiment::rowRanges(scCNA)

    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fri Jun 25 13:22:01 2021
    # overdispersion ----
    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fri Jun 25 13:22:10 2021

    message("Calculating overdispersion.")

    overdisp <- BiocParallel::bplapply(dat_bin,
        overdispersion,
        BPPARAM = BPPARAM
    )

    overdisp <- unlist(overdisp)

    SummarizedExperiment::colData(scCNA)$overdispersion <- overdisp

    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fri Jun 25 13:22:25 2021
    # Breakpoint count
    # Performed for every chromosome
    # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fri Jun 25 13:22:34 2021

    scCNA <- .countBreakpoints(scCNA)

    message("Done.")

    return(scCNA)
}