R/Fardeep.R

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

#' FARDEEP
#' FARDEEP helps users to Estimate of cellular fractions
#' @param signature  A data-frame containing signatures of different cell types.
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @importFrom FARDEEP fardeep
#' @return A data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#'
#'  Bulk <- Bulk_GSE60424
#'  res <- Fardeep(bulkdata = Bulk,
#'                 signature=LM22)
#'
#'




Fardeep <- function(signature, bulkdata) {
  res <- FARDEEP::fardeep(X = signature,
                          Y = bulkdata,
                          alpha1 = 0.1,
                          alpha2 = 1.5,
                          up = 10,
                          low = 1,
                          nn = TRUE,
                          intercept = TRUE,
                          lognorm = TRUE,
                          permn = 100,
                          QN = FALSE)

  res_Fardeep <- res$abs.beta

  return(res_Fardeep)
}