SaveClustersToFCS: Write FlowSOM clustering results to the original FCS files

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

Write FlowSOM clustering results to the original FCS files

Description

Write FlowSOM clustering results to the original FCS files

Usage

SaveClustersToFCS(
  fsom,
  originalFiles,
  preprocessedFiles = NULL,
  selectionColumn = NULL,
  silent = FALSE,
  outputDir = ".",
  suffix = "_FlowSOM.fcs",
  ...
)

Arguments

fsom	FlowSOM object as generated by BuildSOM
originalFiles	FCS files that should be extended
preprocessedFiles	FCS files that correspond to the input of FlowSOM, If NULL (default), the originalFiles are used.
selectionColumn	Column of the FCS file indicating the original cell ids. If NULL (default), no selection is made.
silent	If FALSE (default), print some extra output
outputDir	Directory to save the FCS files. Default to the current working directory (".")
suffix	Suffix added to the filename. Default _FlowSOM.fcs
...	Options to pass on to the read.FCS function (e.g. truncate_max_range)

Value

Saves the extended FCS file as [originalName]_FlowSOM.fcs

Examples

fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                      scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10)
SaveClustersToFCS(flowSOM.res, fileName)

saeyslab/FlowSOM documentation built on April 15, 2024, 1:03 p.m.