Hi there I'm trying to analyze a cancer dataset using xCell (https://github.com/dviraran/xCell) in R. The xCell performs cell type enrichment analysis from gene expression data and provides a accurate and sensitive way to identify enrichment of multiple cell types in an admixture. The problem that I faced is with MulticoreParam. After running the initial code, which is xCellAnalysis, the analysis stopped by a warning. The warning is related to MulticoreParam(), which not work on Windows. I don't know how to change the function code in order to avoid the following warning : MulticoreParam() not supported on Windows, use SnowParam().

Here is the codes and results:

# call the xCell package
> library(xCell)

# Check the input data
> head(AMLexpr[1:5,1:5])
             2803     2805     2806     2807     2808
A1BG     9.319523 7.798598 8.415356 9.043970 8.111895
A2M      9.467271 6.827417 6.528420 9.034234 8.765476
NAT1     8.337392 8.237841 8.153449 7.727084 7.858645
NAT2     6.010205 6.010205 6.167216 6.010205 6.010205
SERPINA3 6.298155 6.010205 6.010205 6.800231 6.010205

# Run the 1st function

xCellAnalysis <- function(expr, signatures=NULL, genes=NULL, spill=NULL, rnaseq=TRUE, file.name = NULL, scale=TRUE,
                          alpha = 0.5, save.raw = FALSE, parallel.sz = 4, parallel.type = 'SOCK',
                          cell.types.use = NULL) {
  if (is.null(signatures))
    signatures = xCell.data$signatures
  if (is.null(genes))
    genes = xCell.data$genes
  if (is.null(spill)) {
    if (rnaseq==TRUE) {
      spill = xCell.data$spill
    } else {
      spill = xCell.data$spill.array
    }
  }

  # Caulcate average ssGSEA scores for cell types
  if (is.null(file.name) || save.raw==FALSE) {
    fn <- NULL
  } else {
    fn <- paste0(file.name,'_RAW.txt')
  }

  if (!is.null(cell.types.use)) {
    A = intersect(cell.types.use,rownames(spill$K))
    if (length(A)<length(cell.types.use)) {
      return ('ERROR - not all cell types listed are available')
    }
  }

  scores <- rawEnrichmentAnalysis(expr,signatures,genes,fn, parallel.sz = parallel.sz, parallel.type = 'SOCK')

  # Transform scores from raw to percentages
  scores.transformed <- transformScores(scores, spill$fv, scale)

  # Adjust scores using the spill over compensation matrix
  if (is.null(file.name)) {
    fn <- NULL
  } else {
    fn <- file.name
  }

  if (is.null(cell.types.use)) {
    scores.adjusted <- spillOver(scores.transformed, spill$K, alpha,fn )
    scores.adjusted = microenvironmentScores(scores.adjusted)
  } else {
    scores.adjusted <- spillOver(scores.transformed[cell.types.use,], spill$K, alpha,fn )
  }
  return(scores.adjusted)
}

# Perform xCell analysis
> adjusted <- xCellAnalysis(AMLexpr)


#result !!  
[1] "Num. of genes: 10786" Setting parallel calculations through a MulticoreParam back-end with workers=4 and tasks=100. Estimating ssGSEA scores for 489 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..."   |====                |   6%Called from: eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP)) 

Warning message: In MulticoreParam(progressbar = verbose, workers = parallel.sz,  :   MulticoreParam() not supported on Windows, use SnowParam()