GdClean: Removing Gd contamination in CyTOF data.

In JunweiLiu0208/GdClean: Method for removing Gadolinium contamination in CyTOF data

Description

Removing Gd contamination in CyTOF data.

Usage

GdClean(fs, gdRatio = NULL, method = "1DNorm")

Arguments

fs	The flowSet object of contaminated CyTOF files.
gdRatio	The selected intensity ratios across Gd channels, default with natural Gd isotope abundance ratios
method	The method used for calculating contamination coefficients for each cell, default with '1DNorm', available options are '1DNorm','2DNorm','Min','Mean','Median'

Value

The flowSet object of cleaned CyTOF files.

Examples

library(GdClean)

fcs.dir <- "../fcsData/"
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")

PercentList <- seq(5, 100, 5)
GdRatios <- estimateGdRatio(ff[[1]], percentList)

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

JunweiLiu0208/GdClean documentation built on Jan. 13, 2022, 8:32 p.m.