R/MIXTURE.R

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

#' Deconvolution Methods MIXTURE
#' MIXTURE 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.
#' @param ncore Default is 1L.
#' @importFrom MIXTURE MIXTURE GetMixture nu.svm.robust.RFE
#' @import  MIXTURE
#' @return A data frame of Mixed cellular fractions.
#' @export
#'
#' @examples
#'
#' Bulk <- Bulk_GSE60424
#' res <- Mixture(bulkdata = Bulk, signature = LM22 )
#'




Mixture <- function(signature , bulkdata, ncore = 1L) {

  require(MIXTURE)

  #### "none" or ,"SingleSubjectTest",PopulationBased"
  mix.test1 <- MIXTURE::MIXTURE(expressionMatrix = as.matrix(bulkdata),
                                signatureMatrix = signature,
                                iter = 50,   ####rep times
                                functionMixture = MIXTURE::nu.svm.robust.RFE,
                                useCores = ncore,
                                verbose = TRUE,
                                nullDist = "PopulationBased")


  res_Mixture <- MIXTURE::GetMixture(mix.test1, type = "absolute")

  return(res_Mixture)
}