gh_apply_to_new_fcs: Construct a 'GatingSet' using a template and FCS files

In RGLab/flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Construct a GatingSet using a template and FCS files

Description

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.

Usage

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.

RGLab/flowWorkspace documentation built on March 17, 2024, 2:24 p.m.