R/SCRS_snr.R

In gongyh/RamanD2O: RamanD2O: an R/Shiny app designed for the analysis of cellular Ramanome data

## calc SNR of SCRS (after preprocess)

SCRS_snr <- function(input_csv, output_dir) {
  input_csv <- args[1] # SCRS data
  output_dir <- args[2] # store snr results

  dir.create(output_dir)

  SNR1 <- read.table(input_csv, header = TRUE, sep = ",")
  SNR2 <- SNR1[, 12:length(SNR1[1, ]) - 1]
  colnames(SNR2) <- formatC(as.numeric(gsub("spc.", "", colnames(SNR2))),
                            digits = 1, format = "f")
  wave_nums <- as.numeric(gsub("[A-Z]", "", colnames(SNR2)))
  SNR_All <- NULL
  for (i in seq_len(nrow(SNR2))) {
    Baseline_start <- which.min(abs(wave_nums - 1730)) # 1760
    Baseline_end <- which.min(abs(wave_nums - 1800)) # 1960
    Baseline <- SNR2[i, Baseline_start:Baseline_end]
    marker <- max(
      SNR2[i, which.min(abs(wave_nums - 3050)):which.min(abs(wave_nums - 2800))]
    ) # C-H peak
    SNR <-
      (marker - sum(Baseline) / length(Baseline)) / sqrt(marker)
    SNR_All <- rbind(SNR_All, SNR)
  }
  SNR_All <- cbind(SNR1[, 1:7], data.frame(SNR = SNR_All))
  write.table(
    SNR_All,
    file = paste0(output_dir, "/", "SNR.txt"),
    sep = "\t",
    quote = FALSE,
    row.names = FALSE
  )
}