how to bring in the cells in a gate from openCyto into the CATALYST pipeline (flow cytometry)

Question

[msn]

Hello all my cytometry friends,

I have some fcs files and I can run them through the CATALYST pipeline no errors. But I dont want to run all the cells. Need to clean up just single cells and only live cells, and only cells with X marker. The tutorial does show how to use gating through opencyto , and that works fine. I get no errors making my gates through opencyto and ggctyo. Everything looks great.

BUT

How do I pass the cells from gate into CATALYST? there doesnt seem to be a way to export those cells (or really conserve the sample and groups).

Thanks for any help you can offer.

https://www.bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/preprocessing.html <- 7.4

https://www.bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/differential.html <- pipeline

Answer 1

[msn]

Solved it.

tl/dr: gh_pop_get_data() will let you export the cells from a gateset from flowWorkspace.

this is not in either the openCyto, ggcyto, or CATAYLST tutorials even though I believe this is a pretty obvious next step function to all these packages. I think I am going to submit a push to the repos to add this in.