AggregateFlowFrames: Aggregate multiple FCS files together

View source: R/0_FlowSOM.R

AggregateFlowFramesR Documentation

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)


saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.