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

# S3 method for default
cytobank_to_gatingset(x, FCS, trans = NULL, ...)

# S3 method for 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

if (FALSE) { 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]]) }