flowDensity loop on flowSet

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beshea.jj • 0

@besheajj-18337

Last seen 6.1 years ago

I have been gating my fcs file by using flowDensity. However- I have gotten to a point where I need to analyze closer to 10-20 fcs files. I've tried looping flowDensity with fsApply:

something like- fsApply(fs, flowdensity()) as well as fsApply(fs, Saved Flow Density Gate)

I have also tried to for loop the flowDensity parameters over the flowSet but none of this seems to work. Is there a way to gate the fcs files with the same flowDensity gate? Otherwise the flowSet is useless since i would have to parse out each single fcs file anyway. I hope this makes sense and would be happy to follow up with more information if needed.

JB

flowdensity flowcore for loop • 1.4k views

ADD COMMENT • link updated 5.9 years ago by Bioconductor Community 0 • written 6.1 years ago by beshea.jj • 0

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Entering edit mode

You should be able to turn your gate into a function and use fsApply to apply that function to all of the flowFrames in your flowSet:

gate.function <- function(x){flowDensity(x, channels = c("FSC-A","FSC-H"),position = c(F,F), percentile =c(.99,.99), use.percentile = c(T,T), ellip.gate = T, scale = .99)}

fsApply(my.flowset, gate.function)

ADD REPLY • link 5.8 years ago mahlon • 0

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