Skip to contents

Run Cell Deconvolution on Bulk RNA-seq from VISTA Object

run_cell_deconvolution.Rd

Estimates cell-type proportions in bulk RNA-seq using single-cell reference or xCell2.

Usage

run_cell_deconvolution(
  x,
  method = c("xCell2"),
  single_cell_reference = NULL,
  reference_labels = NULL,
  gene_id_type = c("auto", "symbol", "ensembl", "ensembl_symbol"),
  xcell2_reference = NULL,
  xcell2_min_shared_genes = NULL,
  transform = c("log2", "raw"),
  ...
)

Arguments

x

A VISTA object.

method

Deconvolution method. Currently only "xCell2" is supported.

single_cell_reference

Reserved for future reference-based methods (ignored).

reference_labels

Reserved for future reference-based methods (ignored).

gene_id_type

Type of gene identifiers: "auto", "symbol", "ensembl", or "ensembl_symbol".

xcell2_reference

Optional xCell2 reference object or dataset name (e.g., "DICE_demo.xCell2Ref"). Used when xCell2 exposes xCell2Analysis().

xcell2_min_shared_genes

Optional numeric shortcut for xCell2's minSharedGenes argument (when supported by the installed xCell2 API).

transform

Expression transformation: "log2" or "raw".

...

Additional arguments passed to the specific method.

Value

VISTA object with cell_fractions added to metadata.

Examples

v <- example_vista()
if (requireNamespace('xCell2', quietly = TRUE)) {
  out <- try(run_cell_deconvolution(v, method = 'xCell2'), silent = TRUE)
  if (!inherits(out, 'try-error')) out
}
#> Starting xCell2 Analysis...