cytobank_to_gatingset: A wrapper that parses the gatingML and FCS files (or...

In RGLab/CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing

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 process

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)

RGLab/CytoML documentation built on Feb. 1, 2024, 12:34 a.m.