R/quanTIseq.R

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

#' Deconvolution Methods QuanTIseq
#' QuanTIseq helps users to Estimate of cellular fractions.
#' @param bulkdata A matrix with genes in rows and samples in columns.
#' @param signature A data-frame containing signatures of different cell types,
#' Default is NULL.
#' @param tumor  Default is TURE
#' @importFrom immunedeconv deconvolute
#' @return data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#'
#'
#'  Bulk <- Bulk_GSE60424
#' res <- Quantiseq(bulkdata = Bulk )
#'



Quantiseq <- function(bulkdata, tumor = TRUE) {
  res <- immunedeconv::deconvolute(gene_expression = bulkdata,
                                   method = "quantiseq",
                                   indications = NULL,
                                   tumor = tumor,
                                   arrays = FALSE,
                                   column = "gene_symbol",
                                   rmgenes = NULL,
                                   scale_mrna = TRUE,
                                   expected_cell_types = NULL)
  res <- t(res)
  colnames(res) <- res[1, ]
  res_Quantiseq <- as.data.frame(res[-1, ])

  return(res_Quantiseq)
}