deconvolute_bseqsc: Deconvolution Analysis using BSeq-sc

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

Deconvolution Analysis using BSeq-sc

Description

Deconvolution Analysis using BSeq-sc

Usage

deconvolute_bseqsc(
  bulk_gene_expression,
  signature = NULL,
  log = NULL,
  ...,
  verbose = FALSE
)

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. If NULL then a built-in reference for pancreatic islet cell sub-population is used (data PancreasIslet in bseqsc package).
log	Logical that indicates if the data x is in in log-scale. If NULL, then log scale is inferred by xbioc::is_logscale.
...	Other arguments passed to CIBERSORT.
verbose	Whether to produce an output on the console.

Value

A list including:

coef	The matrix of estimated proportions (cell type x samples).
stats	The statistics computed by CIBERSORT.

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