Calculates the decomposition using the dwls algorithm — deconvolute

generates a reference profile based on single-cell data. Learns a transformation of bulk expression based on observed single-cell proportions and performs NNLS regression on these transformed values to estimate cell proportions.

deconvolute_dwls(
  bulk_gene_expression,
  signature,
  dwls_submethod = c("DampenedWLS", "OLS", "SVR"),
  verbose = FALSE,
  ...
)

Arguments

bulk_gene_expression: An Expression Set containing bulk data.
signature: The Signature matrix.
dwls_submethod: Three alternative methods in DWLS: OLS, SVR, and DampenedWLS.
verbose: Whether to produce an output on the console.
...: Additional arguments, silently ignored. Allows extra parameters (e.g. dwls_method) to pass through the deconvolute() dispatcher without error.

Value

A matrix of cell type proportion estimates with cell types as rows and individuals as columns.