deconvolute_momf: Deconvolution Analysis using MOMF (via Nonnegative...

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

Deconvolution Analysis using MOMF (via Nonnegative Factorization)

Description

Deconvolution Analysis using MOMF (via Nonnegative Factorization)

Usage

deconvolute_momf(
  bulk_gene_expression,
  signature,
  single_cell_object,
  verbose = FALSE,
  method = "KL",
  ...
)

Arguments

bulk_gene_expression	A matrix of bulk data. Rows are genes, columns are samples. Row and column names need to be set.
signature	The signature matrix. Rows are genes, columns are cell types.
single_cell_object	A matrix with the single-cell data. Rows are genes, columns are samples. Row and column names need to be set.
verbose	Whether to produce an output on the console.
method	Determines which divergence to use. Options: Kullback-Leibler "KL", Itakura-Saito "IS". Defaults to "KL"
...	additional parameters

Value

results object of the MOMF tool. Cell-type proportions can be accessed with $cell.prop

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