Deconvolution Analysis using BSeq-sc

Deconvolution Analysis using BSeq-sc

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.