cytobank_to_gatingset {CytoML} | R Documentation

## A wrapper that parses the gatingML and FCS files (or `cytobank_experiment` object) into GatingSet

### Description

A wrapper that parses the gatingML and FCS files (or `cytobank_experiment` object) into GatingSet

### Usage

    ## Default S3 method:
    cytobank_to_gatingset(x, FCS, trans = NULL, ...)

    ## S3 method for class 'cytobank_experiment'
    cytobank_to_gatingset(x, panel_id = 1, ...)

### Arguments

`x` | the cytobank_experiment object or the full path of gatingML file
`FCS` | FCS files to be loaded
`trans` | a 'transfomerList' object to override the transformations from gatingML files. it is typically used by 'cytobank_experiment' parser(i.e. 'cytobank_to_gatingset.cytobank_experiment') to use the scales info recorded in yaml file.
`...` | other arguments
`panel_id` | select panel to parse

### Value

a GatingSet

### Examples

    ## Not run:
    acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")
    ce <- open_cytobank_experiment(acsfile)
    xmlfile <- ce$gatingML
    fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)
    gs <<- cytobank_to_gatingset(xmlfile, fcsFiles)
    library(ggcyto)
    autoplot(gs[[1]])

    ## End(Not run)

[Package CytoML version 2.0.5 Index]