renaming flow frames in a flowSet using flowCore

Question

[imdoingascience]

I'm working with flow cytometry data and I'm reading a set of FCS files into a flowSet using flowCore. By default the individual frames for the FCS files are named with the file name of the FCS file which is long and cumbersome. I would like to rename the frames in the flowSet object without changing the filenames (or copying them and renaming the copies) Is there anyway to do this? I could not find an explanation on how to rename frames in the flowCore documentation. This is what I have tried:

fs <- read.flowSet(sample_files, emptyValue=F, identifier=str_extract(sample_files,'sample_\\d+\\.fcs$'))

However the frames are still identified by the full cumbersome file name instead of a shorter string. Is there a way to rename them during the call to read.flowSet or rename them after the flowSet object is created?

[Kevin Blighe]

Have you taken a look at the pData() slot for fs? Otherwise, try running str(fs) to see how the internal objects are structured and arranged.

Answer 1

[jaro.slamecka]

I think the key could be changing the GUID of each flowFrame, however, the method sampleNames() should take care of it, after you load the flowSet:

sampleNames(fs) = str_extract(sample_files,'sample_\\d+\\.fcs$')

[imdoingascience]

This worked! Thank you!

For future reference I did the following:

sampleNames(fs) <- str_extract(sample_files,'sample_\\d+\\.fcs$')
pData(fs)$name <- str_extract(sample_files,'sample_\\d+\\.fcs$')

This changes the flow frame reference in the flowset object and changing the name field in pData changes how ggcyto labels the plots. sampleNames is part of the flowWorkspace package.

[Kevin Blighe]

Please mark as Accepted (the answer)