Extract the signature matrix from a Rectangle model — extract_signature

Calls get_signature_matrix() on the RectangleSignatureResult object stored in the signature pickle, returning a standard R matrix. This allows inspection of the selected marker genes and comparison with signatures from other methods. The matrix can be saved for later use with saveRDS().

extract_signature_rectanglepy(
  signature,
  include_mrna_bias = TRUE,
  verbose = FALSE
)

Arguments

signature: Path to a .pkl file created by build_model_rectanglepy().
include_mrna_bias: Whether to apply mRNA bias correction when computing the signature matrix. Default: TRUE.
verbose: Whether to print progress to the console. Default: FALSE.

Value

A matrix with rows = genes and columns = cell types.