GdClean

This package was designed for removing Gadolinium contamination in the CyTOF system, which was induced by the application of Gadolinium-based Contrast Agents in MRI screening. The deposition of Gd isotopes in tissue cells will contaminate the signal of Gd isotope-conjugated antibodies in the CyTOF system and affect data quality. The details of this method can be found in the published paper ‘GdClean: removal of Gadolinium contamination in mass cytometry data’.

Junwei Liu, Lulu Liu, Saisi Qu, Tongtong Zhang, Danyang Wang, Qinghua Ji, Tian Wang, Hongyu Shi, Kaichen Song, Weijia Fang, Wei Chen, Weiwei Yin, GdClean: removal of Gadolinium contamination in mass cytometry data, Bioinformatics, 2021; btab537, https://doi.org/10.1093/bioinformatics/btab537

Installation

You can install the released version of GdClean from GitHub with:

devtools::install_github("JunweiLiu0208/GdClean")

Example

This is a basic workflow which shows you how to use this package:

library(GdClean)
library(flowCore)
library(stringr)
library(dplyr)
library(RColorBrewer)
library(pheatmap)
library(ggplot2)
library(mgcv)
library(ggpubr)

# load FCS files
# Please input your Gd contaminated Data.
fcs.dir = '../path to input directory/'
frames = lapply(dir(fcs.dir,full.names = T),read.FCS,transformation = F,alter.names = T)
names(frames) <- basename(dir(fcs.dir))
fs = as(frames,'flowSet')

# Plot Pearson's correlation coefficients across Gd channels in each CyTOF files in the flowSet.
p1 = GdCorrHeatmap(fs)
p1

# Estimate Gd Ratios.
PercentList = seq(5,100,5)
# select Gd contaminated flowFrame object for estimating.
ff = fs[[1]] 
GdRatios = estimateGdRatio(ff,PercentList)

# Compare the estimated Ratios with Ratios of natural abundance.
p2 = GdRatioPlot(GdRatios)
p2

# Removing Gd contamination with selected Gd ratio and method for estimating contamination coefficients.
# N_Gd = c(1,1.3831,1.0574,1.6784,1.4770) Natural Gd isotope abundance ratios.
# R_Gd = c(1,1.3084,1.0046,1.7641,1.7144) Estimated ratios calculated with control CYTOF data (Gd_Non_Ab).

gdRatio = GdRatios['5%',]
method = '1DNorm'
fs_Clean = GdClean(fs,gdRatio = gdRatio,method = method)

# Write Fcs Files after Gd Clean
inputName = dir(fcs.dir,full.names = F)
outputName = unlist(sapply(inputName, function(x){
  t1 = str_split(x,'.fcs')
  t2 = paste0(t1[[1]][1],'_GdClean.fcs')
  t2
}))

# write the cleaned files into the output directory 
write.flowSet(fs_Clean,outdir = '../path to output directory',outputName)