This uses a GatingHierarchy as a template to apply to other loaded samples in the form of a list of FCS files, resulting in a GatingSet. The transformations and gates from the template are applied to all samples.

gh_apply_to_new_fcs(
  x,
  files,
  swap_cols = FALSE,
  backend = get_default_backend(),
  compensation_source = "sample",
  ...
)

Arguments

x

GatingHierarchy

swap_cols

for internal usage

backend

the backend storage mode to use for load_cytoset_from_fcs

compensation_source

One of the following options:

  • "sample" -- each cytoframe will be compensated with the spillover matrix included in its own FCS

  • "template" -- all cytoframes will be compensatied with the spillover matrix of the template GatingHierarchy

  • "none" -- no compensation will be applied

...

other arguments passed to load_cytoset_from_fcs

Details

This method is still included to support legacy scripts but will deprecated for the more modular workflow of loading a cytoset via load_cytoset_from_fcs followed by gh_apply_to_cs.