cellranger_metrics.R

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## Script name: concatenating cellranger metrics for all the samples
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## Author: Jiekun (Jackie) Yang
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## Date Created: 2022-12-12
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## Email: jkyang@mit.edu
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### cellranger_input_file is a tab delimited file with three columns: folder_path, library_ID and sample_ID
### target_folder is where you would like to store output files generated by this function

## function
cellranger_metrics <- function(cellranger_input_file = NULL, target_folder = NULL) {
  temp.pwd <- getwd()
  cellranger_input <- read.table(cellranger_input_file, header = T, stringsAsFactors = F)
  setwd(target_folder)
  temp.df <- data.frame()
  for (temp.row in 1:nrow(cellranger_input)) {
    temp.path <- cellranger_input[temp.row, 1]
    temp.lib <- cellranger_input[temp.row, 2]
    print(temp.lib)
    temp.df.out <- read.csv(file = paste0(temp.path, "/metrics_summary.csv"), header = T)
    temp.df.out$library <- temp.lib
    temp.df <- rbind(temp.df, temp.df.out)
  }
  write.table(temp.df, paste0(target_folder, "/cellranger_metrics.txt"), sep = "\t", quote = F, col.names = T, row.names = F)
  setwd(temp.pwd)
}