openCyto (version 1.10.3)

add_pop: 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 = "A+", parent, dims = NA, gating_method,
  gating_args = NA, collapseDataForGating = NA, groupBy = NA,
  preprocessing_method = NA, preprocessing_args = NA, ...)

Arguments

gs

GatingSet or GatingSetList

alias,pop,parent,dims,gating_method,gating_args,collapseDataForGating,groupBy,preprocessing_method,preprocessing_args

see details in gatingTemplate

...

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

# 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")