gating {openCyto} | R Documentation

## Apply the gates to a GatingSet

### Description

It applies the gates to the GatingSet based on the population tree described in graphGML.

It loads the gating methods by topological order and applies them to `GatingSet`.

### Usage

    gating(x, y, ...)

    ## S4 method for signature 'gatingTemplate,GatingSet'
    gating(x, y, env_fct = NULL, ...)

    ## S4 method for signature 'gatingTemplate,GatingSetList'
    gating(x, y, env_fct = NULL, ...)

    ## S4 method for signature 'boolMethod,GatingSet'
    gating(x, y, ...)

    ## S4 method for signature 'polyFunctions,GatingSet'
    gating(x, y, ...)

    ## S4 method for signature 'refGate,GatingSet'
    gating(x, y, ...)

### Arguments

`x` | a `gatingTemplate` object
`y` | a `GatingSet` object
`...` | start a `character` that specifies the population (correspoding to 'alias' column in csv template) where the gating process will start from. It is useful to quickly skip some gates and go directly to the target population in the testing run. Default is "root". stop.at a `character` that specifies the population (correspoding to 'alias' column in csv template) where the gating prcoess will stop at. Default is NULL, indicating the end of gating tree. keep.helperGatesa `logical` flag indicating whether to keep the intermediate helper gates that are automatically generated by openCyto. Default is TRUE. 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")
`env_fct` | a `environment` that contains `fcTree` object named as 'fct'. If NULL (by default), no `fcTree` will be constructed. It is currently reserved for the internal debugging.

### Value

Nothing. As the side effect, gates generated by gating methods are saved in `GatingSet`.

### Examples

    ## Not run:
     gt <- gatingTemplate(file.path(path, "data/ICStemplate.csv"), "ICS")
     gs <- GatingSet(fs) #fs is a flowSet/ncdfFlowSet
     gating(gt, gs)
     gating(gt, gs, stop.at = "v") #proceed the gating until population 'v'
     gating(gt, gs, start = "v") # start from 'v'
     gating(gt, gs, parallel_type = "multicore", mc.cores = 8) #parallel gating using multicore
     #parallel gating by using cluster
     cl1 <- makeCluster (8, type = "MPI")
     gating(gt, gs, parallel_type = "cluster", cl = cl1)
     stopCluster ( cl1 )

    ## End(Not run)

[Package openCyto version 1.20.2 Index]