gs_add_gating_method: apply a gating method to the 'GatingSet'

In RGLab/openCyto: Hierarchical Gating Pipeline for flow cytometry data

apply a gating method to the GatingSet

Description

When interacting with the existing gated data, this function provides an alternative way to interact with the GatingSet by supplying the gating description directly through arguments without the need to write the complete csv gating template.

Usage

gs_add_gating_method(
  gs,
  alias = "*",
  pop = "+",
  parent,
  dims = NA,
  gating_method,
  gating_args = NA,
  collapseDataForGating = NA,
  groupBy = NA,
  preprocessing_method = NA,
  preprocessing_args = NA,
  strip_extra_quotes = FALSE,
  ...
)

Arguments

gs	GatingSet or GatingSetList
alias, pop, parent, dims, gating_method, gating_args, collapseDataForGating, groupBy, preprocessing_method, preprocessing_args	see details in gatingTemplate
strip_extra_quotes	logical Extra quotes are added to strings by fread. This causes problems with parsing R strings to expressions in some cases. Default FALSE for usual behaviour. TRUE should be passed if parsing gating_args fails.
...	other arguments mc.cores passed to multicore package for parallel computing parallel_type character specifying the parallel type. The valid options are "none", "multicore", "cluster". cl cluster object passed to parallel package (when parallel_type is "cluster")

Details

Calls to gs_add_gating_method can also be easily reversed with gs_remove_gating_method. Note, however, that it is not possible to differentiate between different GatingSet objects loaded from the same directory with load_gs within a session. Thus, to guarantee a clean history for gs_remove_gating_method, it is necessary to call gs_add_gating_method_init on the loaded GatingSet immediately after re-loading it. See the documentation for gs_add_gating_method_init for more details. This will not be an issue for GatingSet objects created directly using the constructor.

See Also

gs_remove_gating_method gs_add_gating_method_init

Examples

## Not run: 
# add quad gates 
gs_add_gating_method(gs, gating_method = "mindensity", dims = "CCR7,CD45RA", parent = "cd4-cd8+", pop = "CCR7+/-CD45RA+/-")

# polyfunctional gates (boolean combinations of exsiting marginal gates)
gs_add_gating_method(gs, gating_method = "polyFunctions", parent = "cd8", gating_args = "cd8/IFNg:cd8/IL2:cd8/TNFa")

#boolGate method
gs_add_gating_method(gs, alias = "IL2orIFNg", gating_method = "boolGate", parent = "cd4", gating_args = "cd4/IL2|cd4/IFNg") 

## End(Not run)

RGLab/openCyto documentation built on Nov. 7, 2024, 9:23 p.m.