I am trying to gate a flowSet and then take the gateSet and export it to separate fcs files, which should have only the data I chose to gate.

My commands are as follow.

####Read the fcs files with the names i want####

s <- read.flowSet(path = path,files = secondary_datasets,transformation = FALSE, sep="\t")

####Apply the gating with a custom matrix (mat) i have created in the parent my user gives previously as input#####

gs <- GatingSet(fs)

bf <- rectangleGate(filterId=id, .gate=mat)

add(gs, bf, parent=parent)

recompute(gs)

#####Then try to export the new FCS files######

write.flowSet(gs@data,outdir = path,"test")

The problem is my newly created FCS files (1_test, 2_test) are the same with the pre-gated ones. I can see that the files in the flowSet are being loaded properly and the gating gives me no errors, so I guess it works properly as well, since it is a couple lines of code. What am I missing?Doesnt the gs@data give me the gated flowSet? How can I get it if not?

Sorry if I didnt make my problem clear enough, I'm not a biologist.

Directly access the S4 object slots with '@' is generally in R (discouraged unless you know exactly what you are doing) because it goes against one of the central principles of Object Orient design of S4: Abstraction.

So basically you should use whatever methods/functions provided by the "flowWorkspace" package to interact with "GatingSet" object, in this case, you want to use 'getData' method. e.g.

fs_gated <- getData(gs, nodeName)

Get more details in 'help(getData)'  and I also recommend you to take a look at the vignettes of both "flowCore" and  'flowWorkspace" package to familiarize yourself with the APIs.