Importing back csv files exported from sce object will not preserve the unique cell id read in CATALYST

[denvercal1234GitHub]

Hi, Helena,

Thank you for the package.

I ran sce$i <- seq(ncol(sce)) as suggested in #181 (thanks for the suggestion) before exporting the sce into FCS files so that each cell will have a unique numeric value (called nColID).

The output of colData(sce) include this nColID:

In FlowJo, I then gated on some population of interest (and make sure that nColID are only linear transformed so the values don't change by FlowJo), then I exported this gated population as "scale values" csv files and read them into R. I expect each cell in this file should now have a unique nColID, but they are not; some nColID values are duplicated.

My goal is to have a way to pull certain cells from my sce object in R that belong to a gated population that I gated in FlowJo. I looked through the documentations, but did not find the solution. Is it possible with CATALYST?

Thank you again for your help.