An R package to unmix flow cytometry data
Author: Christopher Hall, Babraham Institute, UK
https://www.babraham.ac.uk/science-services/flow-cytometry
devtools::install_github("hally166/flowUnmix")
library(flowUnmix)
??flowUnmix
Basic usage:
#load data
controls_data<-read.flowSet(list.files('C:/Spectral unmixing Aurora/Reference Group', full.names=TRUE))
files2unmix<-read.flowSet(list.files("C:/Spectral unmixing Aurora/Group_001", full.names = TRUE, pattern = ".fcs"))
negative_control<-read.FCS('C:/Spectral unmixing Aurora/Unstained (Beads).fcs')
#run unmixing
flowUnmix(fs=files2unmix, cs=Control_Spectrums, unstainedctrl=negative_control, guessPop = TRUE, popCheck = TRUE)
guessPop needs an unstained control.
popCheck displays the spectral signature of the control.
If you want autofluorescence subtraction you can add an extra signature to the controls by gating the autofluorescent cells and passing them as a control.