Getting a dataset that only contains the flow data within the gated area
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henry • 0
@cbb38067
Last seen 7 weeks ago

Hi, I am new to using flow cytometry data and I'm having trouble achieving my goal.

I want to apply a gate to my flow data (.fcs file) and then subset the data to only have the information in that gate. I'm currently using the flowWorkspac package. At first I tried using gs_cyto_data(), gh_pop_get_data(), and gh_pop_get_indices() but I don’t think I am using them properly as I don’t know how do access the gated information only. I would like to be able to plot only the information in the gated subset afterwards.

Any help/suggestions would be appreciated!

Thank you

flowWorkspace • 117 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 7 weeks ago

You didn't post your example code, so here is my best guess of your workflow

> library(flowCore)
> library(flowWorkspace)
> library(openCyto)
> cs <- load_cytoset_from_fcs(system.file("extdata/CytoTrol_CytoTrol_1.fcs", package = "flowWorkspaceData"))
> gs = GatingSet(cs)
> gs_get_pop_paths(gs)
[1] "root"
> gs_add_gating_method(gs, "s", parent = "root", dims = "FSC-A,FSC-H", gating_method = "singletGate")
...
done
> gs_get_pop_paths(gs)
[1] "root" "/s"
> # library(ggcyto)
> # autoplot(gs, "s")
> gh = gs[[1]]
> gh_pop_get_stats(gh)
pop  count
1: root 119531
2:   /s 112200
> subset = gh_pop_get_data(gh, "s")
> nrow(subset)
[1] 112200