deconvolute_dwls: Calculates the decomposition using the dwls algorithm

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Calculates the decomposition using the dwls algorithm

Description

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.

Usage

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.

Value

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

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.