Run the minimal downstream workflow
Usage
run_core(
obj,
signatures = c("cytotoxic", "antigen_presentation"),
panels = c("t_cell", "nk", "b_cell", "monocyte", "macrophage", "dendritic"),
signature_sets = NULL,
marker_panels = NULL,
outdir = NULL
)
Arguments
- obj
A scdown_obj.
- signatures
Character vector of signatures to score.
- panels
Character vector of marker panels to use for annotation checks.
- signature_sets
Optional named list of custom signatures.
- marker_panels
Optional named list of custom marker panels.
- outdir
Optional output directory.
Value
A named list of downstream results.