Question: flowDensity loop on flowSet
0
gravatar for beshea.jj
12 months ago by
beshea.jj0
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 • 270 views
ADD COMMENTlink modified 10 months ago by Bioconductor Community ♦♦ 0 • written 12 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)
ADD REPLYlink written 8 months ago by mahlon0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour