In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

knitr::opts_chunk$set(echo = TRUE)

This script downloads and re-formats example data for spillover correction. As test data, we use the files that are provided by the following publication:

Chevrier, Stéphane, Helena L. Crowell, Vito R. T. Zanotelli, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller. 2017. “Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.” Cell Systems 6: 612–20.

They can be accessed from https://data.mendeley.com/datasets/v58yj49pfr/1.

More specificaly, the spillover files are part of Figure S5.

Download the data

Here, we will first download the data.

sm_url <- "https://data.mendeley.com/public-files/datasets/v58yj49pfr/files/b39223d2-2825-4e79-9875-86fa0e1c55d2/file_downloaded?dl=1"

download.file(sm_url, "Figure_S5.zip")
unzip("Figure_S5.zip", overwrite=TRUE)
unlink("Figure_S5.zip")

Read in and subset the data

We will now prepare a subsample of the data for testing purposes:

library(readr)
library(stringr)
full_txt <- list.files("Figure_S5/Spillover_Matrix_1/", pattern = "Dy161|Dy162|Dy163|Dy164", full.names = TRUE)
full_txt_names <- list.files("Figure_S5/Spillover_Matrix_1/", pattern = "Dy161|Dy162|Dy163|Dy164")
full_txt_names <- str_extract(full_txt_names, "^Dy[1-9]{3}")

full_txt <- lapply(full_txt, read_delim, delim = "\t")

## Subset to first 100 rows
full_txt <- lapply(full_txt, function(x){x[seq_len(100),]})

## Subset to specific channels
full_txt <- lapply(full_txt, function(x){x[,colnames(x) %in% 
                                               c("Start_push", "End_push", "Pushes_duration",
                                                 "X", "Y", "Z", "161Dy(Dy161Di)", 
                                                 "162Dy(Dy162Di)", "163Dy(Dy163Di)", "164Dy(Dy164Di)")]})

Write out files

We will now save the processed files.

dir.create("../extdata/spillover")
for (i in seq_len(length(full_txt))) {
    write_delim(full_txt[[i]], 
                file = paste0("../extdata/spillover/", full_txt_names[i], ".txt"),
                delim = "\t")
}