RemoveMargins {PeacoQC} | R Documentation

## Remove margin events of flow cytometry data

### Description

`RemoveMargins` will remove margin events from the flowframe based on the internal description of the fcs file.

### Usage

    RemoveMargins(ff, channels,
    channel_specifications=NULL, output="frame")

### Arguments

`ff` | A flowframe that contains flow cytometry data.
`channels` | The channel indices or channel names that have to be checked for margin events
`channel_specifications` | A list of lists with parameter specifications for certain channels. This parameter should only be used if the values in the internal parameters description is too strict or wrong for a number or all channels. This should be one list per channel with first a minRange and then a maxRange value. This list should have the channel name found back in `colnames(flowCore::exprs(ff))`. If a channel is not listed in this parameter, its default internal values will be used. The default of this parameter is NULL.
`output` | If set to "full", a list with the filtered flowframe and the indices of the margin 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 raw data
    fileName <- system.file("extdata", "111.fcs", package="PeacoQC")
    ff <- flowCore::read.FCS(fileName)

    # Define channels where the margin events should be removed
    channels <- c(1, 3, 5:14, 18, 21)

    # Remove margins

    ff_cleaned <- RemoveMargins(ff, channels)

    # If an internal value is wrong for a channels (e.g. FSC-A)

    channel_specifications <- list("FSC-A"=c(-111, 262144))
    ff_cleaned <- RemoveMargins(
        ff,
        channels,
        channel_specifications=channel_specifications)

[Package PeacoQC version 1.4.0 Index]