R/TIMER.R

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

#' Deconvolution Methods of TIMER
#' TICPE helps users to Estimate of cellular fractions by 23 cancer types gene-markers
#' from The Cancer Genome Atlas (TCGA).
#'  for cell type deconvolution.
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @param tumortype  23 cancer types from The Cancer Genome Atlas (TCGA).
#' @importFrom immunedeconv deconvolute
#' @return Mixed cell composition estimation ratio data frame
#' @export
#'
#'
#' @examples
#'
#' Bulk <- Bulk_GSE60424
#' res <- Timer(bulkdata=Bulk,
#'               tumor = TRUE,
#'               tumortype = "brca")
#'
#'







Timer <- function(bulkdata,
                  tumortype = "brca") {
  indi <- rep(tumortype, time = ncol(bulkdata))
  res <- immunedeconv::deconvolute(gene_expression = bulkdata,
                                   method = "timer",
                                   indications = indi,
                                   tumor = TRUE,
                                   arrays = FALSE,
                                   column = "gene_symbol",
                                   rmgenes = NULL,
                                   scale_mrna = TRUE,
                                   expected_cell_types = NULL)
  res <- t(res)

  colnames(res) <- res[1, ]

  res_Timer <- as.data.frame(res[-1, ])

  return(res_Timer)
}