Re-naming $PnS parameters
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jasonemo • 0
@a255634a
Last seen 7 months ago

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?

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flowCore • 165 views
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SamGG ▴ 270
@samgg-6428
Last seen 8 weeks ago
France/Marseille/Inserm

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!

Created on 2021-03-16 by the [reprex package](https://reprex.tidyverse.org) (v1.0.0)

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