wsx_compMats_to_fcs: Write the compensation matrices generated in a flowjo...

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Write the compensation matrices generated in a flowjo workspace to the SPILL keywords of respective FCS files

Description

The compensation matrices generated or optimized in FlowJo only exist in the workspace. The underlying FCS files remain unchanged. This is part of FlowJos philosophy, FCS remain original all the time. This is actually not a bad procedure but reduces flexibility in some cases. This function saves the associated compensation matrices to the FCS files - the matrices are written into the SPILL keyword. That makes them easily and unambiguously available for other calculations outside of FlowJo (e.g. in R) when compensated channels are required.

Usage

wsx_compMats_to_fcs(ws, groups = NULL, alt_FCS_file_folder = NULL, ...)

Arguments

ws	path to flowjo workspace
groups	which flowjo groups to get fcs files from
alt_FCS_file_folder	if FCS files paths on disk are not the same as in flowjos wsp file, then provide the correct path here
...	additional arguments to fcexpr:::prep_spill()

Value

no return but SPILL keyword updated in FCS files

Examples

## Not run: 
wsx_compMats_to_fcs(ws = "mypath/my.wsp")

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.