Deconvolute using CIBERSORT or CIBERSORT abs.

Deconvolute using CIBERSORT or CIBERSORT abs.

deconvolute_cibersort(
  gene_expression_matrix,
  arrays,
  absolute = FALSE,
  abs_method = "sig.score",
  ...
)

Arguments

gene_expression_matrix

a m x n matrix with m genes and n samples

arrays

Set to TRUE if working with Microarray data instead of RNA-seq. As recommended by the authors, quantile normalization will be enabled for Microarrays and disabled for RNAseq.

absolute

Set to TRUE for CIBERSORT absolute mode.

abs_method

Choose method to compute absolute score (only if absolute=TRUE).

...

passed through to the original CIBERSORT function. A native argument takes precedence over an immunedeconv argument (e.g. QN takes precedence over arrays). Documentation is not publicly available. Log in to the CIBERSORT website for details.