add_pop {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

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")

Details

Calls to add_pop can also be easily reversed with remove_pop. 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 remove_pop, it is necessary to call add_pop_init on the loaded GatingSet immediately after re-loading it. See the documentation for add_pop_init for more details. This will not be an issue for GatingSet objects created directly using the constructor.

See Also

remove_pop add_pop_init

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 1.22.0 Index]