R/EPIC.R

In libcell/deconvBench: A tool for approaches evaluation of cell fraction estimation

#' Deconvolution Methods of EPIC
#' EPIC helps users to Estimate of cellular fractions.
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @importFrom EPIC EPIC
#' @return A data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#' Bulk <- Bulk_GSE60424
#' res <- Epic(bulkdata = Bulk )
#'




Epic <- function(bulkdata) {
  res <- EPIC::EPIC(bulk = bulkdata,
              mRNA_cell = NULL,
              mRNA_cell_sub = NULL,
              sigGenes = NULL,
              scaleExprs = TRUE,
              withOtherCells = TRUE,
              constrainedSum = TRUE,
              rangeBasedOptim = FALSE)

  res_Epic <- res$cellFractions

  print(res_Epic)

  return(res_Epic)
}