R/TICPE.R

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

#' Deconvolution Methods of TICPE
#' TICPE helps users to Estimate of cellular fractions by three references
#'  for cell type deconvolution.
#'
#' @import TICPE
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @param tumortype one of four methods, inclusd of "CRC", "lung","SKCM".
#'
#'
#' @return Mixed cell composition estimation ratio data frame.
#' @export
#'
#' @examples
#'
#' Bulk <- Bulk_GSE60424
#' res <- Ticpe (bulkdata=Bulk,
#'               tumortype = "CRC")
#'



Ticpe <- function(bulkdata, tumortype = "CRC") {

  if (tumortype == "CRC") {
    CRC_select_siggene <- TICPE::CRC_select_siggene
    CRC_stable_pairs <- TICPE::CRC_stable_pairs
    CRC_parameter <- TICPE::CRC_parameter
    TICPE_res <- TICPE::TICPEScores(bulkdata,  # bulk_data
                                    CRC_select_siggene,   # gene_list
                                    CRC_stable_pairs,     # higher and lower genes.
                                    CRC_parameter,        # Stimulatedmodel
                                    0.5)
  } else

    if (tumortype == "lung") {
      lung_select_siggene <- TICPE::lung_select_siggene
      lung_stable_pairs <- TICPE::lung_stable_pairs
      lung_parameter <- TICPE::lung_parameter
      TICPE_res <- TICPE::TICPEScores(bulkdata,  #bulk_data
                                      lung_select_siggene,   # gene_list
                                      lung_stable_pairs,     # higher and lower genes.
                                      lung_parameter,        # Stimulatedmodel
                                      0.5)
  } else

    if (tumortype == "SKCM") {
      skcm_select_siggene <- TICPE::skcm_select_siggene
      skcm_stable_pairs <- TICPE::skcm_stable_pairs
      skcm_parameter <- TICPE::skcm_parameter
      TICPE_res <- TICPE::TICPEScores(bulkdata,  #bulk_data
                                      skcm_select_siggene,    # gene_list
                                      skcm_stable_pairs,     # higher and lower genes.
                                      skcm_parameter,        # Stimulatedmodel
                                      0.5)
    } else {
      TICPE_res <- NULL
    }


  res_Ticpe <- TICPE_res

  return(res_Ticpe)
}