RemoveDoublets: Remove doublet events from flow cytometry data

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

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)

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