SaveClustersToFCS: Write FlowSOM clustering results to the original FCS files

View source: R/2_buildSOM.R

SaveClustersToFCSR Documentation

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 July 6, 2024, 10:59 a.m.