AlternativeFunction-nQuack

process_data_chrom

process_data_chrom <- function(file, min.depth = 2, max.depth.quantile.prob = 0.9,
                               error = 0.01, trunc = c(0,0), chrom){
  df <- data.table::fread(file, sep = "\t")
  if(ncol(df) != 7){
    message("Did you run `prepare_data()` on this file? Your data is in the wrong format, please correct and try again.")
  } else{
    df <- df[which(df$chr == chrom), 3:7]
    df <- stats::na.omit(df)
    dfm <- as.matrix(df)
    
    allelefreq <- process_rcpp(dfm, min.depth, max.depth.quantile.prob, trunc, error )
    return(allelefreq)
  }
}

process_data_chroms <- function(file, min.depth = 2, max.depth.quantile.prob = 0.9,
                               error = 0.01, trunc = c(0,0), chroms){
  df <- data.table::fread(file, sep = "\t")
  if(ncol(df) != 7){
    message("Did you run `prepare_data()` on this file? Your data is in the wrong format, please correct and try again.")
  } else{
    df <- df[which(df$chr %in% chroms), 3:7]
    df <- stats::na.omit(df)
    dfm <- as.matrix(df)
    
    allelefreq <- process_rcpp(dfm, min.depth, max.depth.quantile.prob, trunc, error )
    return(allelefreq)
  }
}