AggregateFlowFrames: Aggregate multiple FCS files together

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

Aggregate multiple FCS files together

Description

Aggregate multiple FCS files to analyze them simultaneously. A new FCS file is written, which contains about cTotal cells, with ceiling(cTotal/nFiles) cells from each file. Two new columns are added: a column indicating the original file by index, and a noisy version of this for better plotting opportunities (index plus or minus a value between 0 and 0.1).

Usage

AggregateFlowFrames(
  fileNames,
  cTotal,
  channels = NULL,
  writeOutput = FALSE,
  outputFile = "aggregate.fcs",
  keepOrder = FALSE,
  silent = FALSE,
  sampleWithReplacement = FALSE,
  ...
)

Arguments

fileNames	Character vector containing full paths to the FCS files or a flowSet to aggregate
cTotal	Total number of cells to write to the output file
channels	Channels/markers to keep in the aggregate. Default NULL takes all channels of the first file.
writeOutput	Whether to write the resulting flowFrame to a file. Default FALSE
outputFile	Full path to output file. Default "aggregate.fcs"
keepOrder	If TRUE, the random subsample will be ordered in the same way as they were originally ordered in the file. Default = FALSE.
silent	If FALSE, prints an update every time it starts processing a new file. Default = FALSE.
sampleWithReplacement	If TRUE and more cells per file are requested than actually present, all cells will be included plus additional resampling. Otherwise, at most all cells will be included once. Default = FALSE.
...	Additional arguments to pass to read.FCS

Value

This function does not return anything, but will write a file with about cTotal cells to outputFile

See Also

ceiling

Examples

# Define filename
fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
# This example will sample 2 times 500 cells.
ff_new <- AggregateFlowFrames(c(fileName, fileName), 1000)

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.