R/OLD_ParsePlateReaderFile.R

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

#' Deprecated plate reader file parser
#' @param plate_reader_file plate reader file from old plate reader
#' @return list that includes data in table format and the number of measurements that the plate reader took per sample
#' @export
#'

Deprecated_ParsePlateReaderFile <- function(plate_reader_file) {
  # Import file
  file <- utils::read.csv(plate_reader_file)
  
  # Find start point
  for (i in 0:ncol(file)) {
    if (length((grep("Well", file[, i]))) > 0) {
      title_row <- grep("Well", file[, i])
      end_row <- grep("Well", file[, i]) + 96
      start_column <- i
    }
	else {
		title_row <- 9
		end_row <- 105
		start_column <- 2
	}
  }
  start_row = title_row + 1
  num_reads = ncol(file) - start_column
  
  # Parse table
  parsed_table <- file[start_row:end_row, start_column:ncol(file)]
  
  
  
  # Add column names
  colnames(parsed_table) <-
    make.names(lapply(file[title_row, start_column:ncol(file)], as.character))
  
  newtable <- rep(0, 96)
  
  rows <- c("A", "B", "C", "D", "E", "F", "G", "H")
  cols <-
    c("01",
      "02",
      "03",
      "04",
      "05",
      "06",
      "07",
      "08",
      "09",
      "10",
      "11",
      "12")
  
  rows_length <- length(rows)
  cols_length <- length(cols)
  
  wells <- "Well"
  for (r in 1:rows_length) {
    for (c in 1:cols_length) {
      index <- (r - 1) * 12 + c
      index_name <- paste(rows[r], cols[c], sep = "")
      wells <- c(wells, index_name)
      
    }
  }
  final_table <-
    dplyr::filter(data.frame(
      ReaderWell = wells[-1],
      Fluorescence = as.numeric(as.character(parsed_table$Read.1))
    ),
    !is.na(Fluorescence))
  
  
  
  
  
  return(final_table)
  
}