Run the standard AEGIS workflow with one function

Convenience entry point that constructs an AEGIS object (if needed) and runs the core audit/comparison pipeline. Supports:

a Seurat object + deconvolution list (single-sample)
a named list of Seurat objects + nested deconvolution list (multi-sample)
an existing aegis or aegis_multi object

Usage

run_aegis(
  x,
  deconv = NULL,
  markers = NULL,
  do_marker = TRUE,
  do_spatial = TRUE,
  do_compare = TRUE,
  do_consensus = TRUE,
  strict = TRUE
)

Arguments

x: A Seurat object, named list of Seurat objects, aegis, or aegis_multi.
deconv: Optional deconvolution input. For single-sample: named list of method matrices. For multi-sample: nested list by sample.
markers: Optional marker list. If provided with an existing AEGIS object, it replaces x$markers.
do_marker: Logical; run audit_marker().
do_spatial: Logical; run audit_spatial().
do_compare: Logical; run compare_methods().
do_consensus: Logical; run compute_consensus().
strict: Logical; strict validation for multi-sample constructor path.

Value

An aegis or aegis_multi object.