RemoveMargins: Remove margin events of flow cytometry data

In saeyslab/PeacoQC: Peak-based selection of high quality cytometry data

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 vectors 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 in a vector. 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),
                               "SSC-A"=c(-111, 262144))
ff_cleaned <- RemoveMargins(
    ff,
    channels,
    channel_specifications=channel_specifications)

saeyslab/PeacoQC documentation built on Aug. 24, 2023, 8:11 a.m.