Deconvolute using xCell

Deconvolute using xCell

deconvolute_xcell(
  gene_expression_matrix,
  arrays,
  expected_cell_types = NULL,
  ...
)

Arguments

gene_expression_matrix

a m x n matrix with m genes and n samples

arrays

Set to TRUE if microarray data, to FALSE for RNASeq (rnaseq parameter in xCell)

expected_cell_types

a character list of the cell types to use in the analysis. If NULL runs xCell with all cell types. The spillover compensation step may over compensate, thus it is always better to run xCell with a list of cell types that are expected to be in the mixture. The names of cell types in this list must be a subset of the cell types that are inferred by xCell. (cell.types.use parameter in xCell)

...

Passed through to original xCell function. A native argument takes precedence over an immunedeconv argument (e.g. rnaseq takes precedence over arrays) See xCellAnalysis