method to re-load in R a .nc file that has been created with read.ncdfflowset

[mikejiang]

From: Dolcetti, Luigi luigi.dolcetti@kcl.ac.uk
Sent: Sunday, March 8, 2020 10:57 AM
To: Jiang, Mike wjiang2@scharp.org
Subject: ncdfFlow question

Dear Mike,
My name is Luigi and I am setting up an analysis pipeline for flow cytometry data using ncdfFlow.
I am not able to find any method to re-load in R a .nc file that has been created with read.ncdfflowset…. Am I missing something?

[mikejiang]

the nc (or more accurately, hdf5) file generated by ncdfFlowSet is not self-contained file, which only stores the data matrix. All the meta data still resides in R and requires the save_ncfs and load_ncdf functions to fully archive to disk and reload from it.

Also, ncdfFlowSet is now deprecated in favor of the new cytoset introduced in the latest development version of flowWorkspace. Check the vignette here http://bioconductor.org/packages/3.11/bioc/html/flowWorkspace.html