RemoveDoublets {PeacoQC} | R Documentation

## Remove doublet events from flow cytometry data

### Description

`RemoveDoublets` will remove doublet events from the flowframe based on two channels.

### Usage

    RemoveDoublets(ff, channel1="FSC-A", channel2="FSC-H", nmad=4,
    verbose=FALSE, output="frame")

### Arguments

`ff` | A flowframe that contains flow cytometry data.
`channel1` | The first channels that will be used to determine the doublet events. Default is "FSC-A"
`channel2` | The second channels that will be used to determine the doublet events. Default is "FSC-H"
`nmad` | Bandwidth above the ratio allowed (cells are kept if their ratio is smaller than the median ratio + `nmad` times the median absolute deviation of the ratios). Default is 4.
`verbose` | If set to TRUE, the median ratio and width will be printed. Default is FALSE.
`output` | If set to "full", a list with the filtered flowframe and the indices of the doublet event is returned. If set to "frame", only the filtered flowframe is returned. The default is "frame".

### Value

This function returns either a filtered flowframe when the `output` parameter is set to "frame" or a list containing the filtered flowframe and a TRUE/FALSE list indicating the margin events. An extra column named "Original_ID" is added to the flowframe where the cells are given their original cell id.

### Examples

    # Read in data
    fileName <- system.file("extdata", "111.fcs", package="PeacoQC")
    ff <- flowCore::read.FCS(fileName)

    # Remove doublets
    ff_cleaned <- RemoveDoublets(ff)

[Package PeacoQC version 1.2.0 Index]