AggregateFlowFrames: Aggregate multiple fcs files together

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

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,
  writeOutput = FALSE,
  outputFile = "aggregate.fcs",
  writeMeta = FALSE,
  keepOrder = FALSE,
  verbose = FALSE,
  ...
)

Arguments

fileNames	Character vector containing full paths to the fcs files to aggregate
cTotal	Total number of cells to write to the output file
writeOutput	Whether to write the resulting flowframe to a file
outputFile	Full path to output file
writeMeta	If TRUE, files with the indices of the selected cells are generated
keepOrder	If TRUE, the random subsample will be ordered in the same way as they were originally ordered in the file. Default = FALSE.
verbose	If TRUE, prints an update every time it starts processing a new file. 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)

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.