add_pop {openCyto} | R Documentation

## apply a gating method to the `GatingSet`

### Description

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

### Usage

    add_pop(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")

### Examples

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

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

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

    ## End(Not run)

[Package openCyto version 1.20.2 Index]