Since the latest FlowCore update, when I try to rename the $PnS parameters those marker names are not saved to my file when writing FCS files. However, when I rename $PnN parameters the marker names do get saved to file. In an older version of flowcore, I could rename $PnN and $PnS parameters without any problems. Could this be fixed in the next update?
I am not part of RGLab, so this is not an official answer.
Keeping keywords and descriptions is not a simple task. The current approach uses the desc column when writing a flow frame to disk. The keyword $PnS is therefore ignored. Maybe setting $PnS should be forbidden or synchronized with desc. Whatever, here is a code that is currently working. It's not perfect, but it is working.
For the next, try to be more precise than "older version of flowCore".
Best.
library(flowCore)
R.version.string
#> [1] "R version 4.0.3 (2020-10-10)"
packageVersion("flowCore")
#> [1] '2.2.0'
# a sample file
fcsFile <- system.file("extdata", "0877408774.B08", package="flowCore")
## read file and linearize values
samp <- read.FCS(fcsFile, transformation="linearize")
# overview
samp
#> flowFrame object '0877408774.B08'
#> with 10000 cells and 8 observables:
#> name desc range minRange maxRange
#> $P1 FSC-H FSC-H 1024 0.00000 1023
#> $P2 SSC-H SSC-H 1024 0.00000 1023
#> $P3 FL1-H NA 1024 1.00904 10000
#> $P4 FL2-H NA 1024 1.00904 10000
#> $P5 FL3-H NA 1024 1.00904 10000
#> $P6 FL1-A NA 1024 0.00000 1023
#> $P7 FL4-H NA 1024 1.00904 10000
#> $P8 Time Time (51.20 sec.) 1024 0.00000 1023
#> 164 keywords are stored in the 'description' slot
keyword(samp, "$P1S")
#> $`$P1S`
#> [1] "FSC-H"
# change keyword
keyword(samp) = list("$P1S" = "FCS_H_kwd")
keyword(samp)
#> $`$P1S`
#> [1] "FCS_H_kwd"
# change desc field
pData(parameters(samp))$desc[1] = "FSC_H_desc"
samp
#> flowFrame object 'anonymous'
#> with 10000 cells and 8 observables:
#> name desc range minRange maxRange
#> $P1 FSC-H FSC_H_desc 1024 0.00000 1023
#> $P2 SSC-H SSC-H 1024 0.00000 1023
#> $P3 FL1-H NA 1024 1.00904 10000
#> $P4 FL2-H NA 1024 1.00904 10000
#> $P5 FL3-H NA 1024 1.00904 10000
#> $P6 FL1-A NA 1024 0.00000 1023
#> $P7 FL4-H NA 1024 1.00904 10000
#> $P8 Time Time (51.20 sec.) 1024 0.00000 1023
#> 1 keywords are stored in the 'description' slot
# overview
read.FCS(write.FCS(samp, "test.fcs"))
#> flowFrame object 'test.fcs'
#> with 10000 cells and 8 observables:
#> name desc range minRange maxRange
#> $P1 FSC-H FSC_H_desc 1024 0 1023
#> $P2 SSC-H SSC-H 1024 0 1023
#> $P3 FL1-H NA 3653 0 3652
#> $P4 FL2-H NA 9912 0 9911
#> $P5 FL3-H NA 3280 0 3279
#> $P6 FL1-A NA 1024 0 1023
#> $P7 FL4-H NA 9823 0 9822
#> $P8 Time Time (51.20 sec.) 627 0 626
#> 67 keywords are stored in the 'description' slot
# the winning is desc!
