Question: flowDensity loop on flowSet
0
9 months ago by
beshea.jj0 wrote:

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

flowcore flowdensity for loop • 217 views
modified 7 months ago by Bioconductor Community ♦♦ 0 • written 9 months ago by beshea.jj0

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)