cytobank_experiment
object) into GatingSetR/cytobank2GatingSet.R
, R/cytobankExperiment.R
cytobank_to_gatingset.Rd
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, ...)
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 |
a GatingSet
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]]) }