This function processes the demultiplex stats by removing rows with "Undetermined" SampleID and splitting the Index column into two separate columns.

Demultiplex_Stats_proc.R

#' Demultiplex Stats Processing
#'
#' This function processes the demultiplex stats by removing rows with "Undetermined" SampleID and splitting the Index column into two separate columns.
#'
#' @title Process Demultiplex Stats
#' @description Removes rows with "Undetermined" SampleID from the input data frame and splits the Index column into two separate columns (index1 and index2).
#' @param x1 A data frame containing the demultiplex stats. The data frame should have a "SampleID" column and an "Index" column.
#' @importFrom assertthat is.data.frame noNA
#' @return A data frame with the processed demultiplex stats, including the split Index column.
#' @export Demultiplex_Stats_proc
#' @author Satoshi Kume
#' @examples
#' \dontrun{
#' x1 <- read.csv("./Demultiplex_Stats.csv", header = TRUE, check.names = FALSE)[1:12,]
#' result <- Demultiplex_Stats_proc(x1)
#' head(result)
#' }

Demultiplex_Stats_proc <- function(x1){
  assertthat::is.data.frame(x1)
  assertthat::noNA(x1$SampleID)
  assertthat::noNA(x1$Index)

  # Demultiplex: Remove rows with "Undetermined" SampleID
  x1 <- x1[x1$SampleID != "Undetermined",]

  # Split the Index column into two separate columns
  cc <- data.frame(matrix(unlist(strsplit(x1$Index, "-")), ncol = 2, byrow = TRUE))
  y <- data.frame(x1[,1:2],
                  Index=sub("-", "", x1[,3]),
                  index1=cc[,1],
                  index2=cc[,2],
                  x1[,4:ncol(x1)],
                  check.names = FALSE)

  return(y)
}