How to sample a certain number of events from each fcs file and then concatenate

nolanlab / cytofCore

R package for working with CyToF data

GNU General Public License v3.0

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How to sample a certain number of events from each fcs file and then concatenate #10

Open elensyri opened 5 years ago

elensyri commented 5 years ago

Hi there I am looking to concatenate some fcs files. I would like to select a certain number of events (randomly) from the fcs files so there is an equal representation from all the fcs files and then concatenate. Can this be done with this script? If not are you aware of an alternative that can do this? Many thanks. Eleni

rbruggner commented 5 years ago

No - I do not believe the concatenation script supports subsampling. The citrus.readFCSsetfunction does this but does not output concatenated FCS files. https://github.com/nolanlab/citrus/blob/master/R/citrus.util.R

You could definitely combine the two?

elensyri commented 5 years ago

Hay thanks for the prompt reply.

That is a good idea. I was reading the code. A bit confused though I will load the fcs files in Citrus and at which point do I export them again on the code?? Then I assume I can import them in cytofCore for concatenation?