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ImmuneDynamics / Spectre

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
https://immunedynamics.github.io/spectre/
MIT License
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truncate_max_range = FALSE #121

Closed dietmar113 closed 2 years ago

dietmar113 commented 2 years ago

Hi, I got this Warning: 1: In readFCSdata(con, offsets, txt, transformation, which.lines, scale, : Some data values of 'eFluor 450-A' channel exceed its $PnR value 4194304 and will be truncated! To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'

and wanted to avoid the truncation by adding "truncate_max_range = FALSE" to the function: Spectre::read.files(file.loc = InputDirectory, file.type = ".fcs", truncate_max_range = FALSE do.embed.file.names = TRUE)

which does not work.

How will it work?

Thank you,

SamGG commented 2 years ago

Hi, The function in the read.Files.R file has no extra options (...) passed to the read.FCS function. This will not work unless you modify the code yourself, which is easy if you know a little bit of R. Best.

ghar1821 commented 2 years ago

I've added the extra options to read.files. You can now use truncate_max_range parameter which will simply be passed on to flowCore's read.FCS function.

For now, to use it, please install the package version in the development branch using devtools::install_github("immunedynamics/spectre", ref='development')