gs_add_gating_method {openCyto} | R Documentation

## 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)

[Package openCyto version 2.2.0 Index]