R/Toast_no.R

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

#' TOAST no reference
#'
#' @param bulkdata  A matrix with genes in rows and samples in columns.
#' @param celltypenum   Specify the range of underlying subpopulation number.
#' @importFrom TOAST csDeconv
#' @return A data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#'
#'
#'  Bulk <- Bulk_GSE60424
#'  res <- Toast_no(bulkdata = Bulk,
#'                  celltypenum = 5)
#'
#'



Toast_no <- function(bulkdata,celltypenum){

  outRF1 <- TOAST::csDeconv(Y_raw = as.matrix(bulkdata),
                            K = celltypenum,   #The number of cell types.
                            nMarker = 500 ,  #the number of signature used
                            TotalIter = 30,  #rep number across samples
                            bound_negative =  TRUE)# Negative parameter estimates are constrained to be 0

  TOAST_RF_res <- outRF1$estProp

  res_Toast_no <- TOAST_RF_res

  return(res_Toast_no)
}