AggregateFlowFrames {FlowSOM} | R 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,
      ...
    )

### Arguments

`fileNames` | Character vector containing full paths to the fcs files 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.
`...` | 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)

[Package FlowSOM version 2.2.0 Index]