R/mhandler.R

In ngstk: Next-Generation Sequencing (NGS) Data Analysis Toolkit

# Function that can be uesd to process data
mhandler <- function(handler_data, config_input, mhandler_funs = NULL, extra_params = NULL) {
  old_op <- options()
  options(stringsAsFactors = F)
  if (!is.null(mhandler_funs)) {
    for (i in mhandler_funs) {
      handler_data <- do.call(i, list(handler_data = handler_data, config_input = config_input, 
        extra_params = extra_params))
    }
    
  }
  options(old_op)
  return(handler_data)
}

# two colum match
mhandler_fusions_left_match <- function(handler_data, config_input, extra_params = list(gene_5 = 1, 
  left_gene = NULL, fusions_left_match_flag = TRUE)) {
  left_gene <- extra_params$left_gene
  gene_5 <- extra_params$gene_5
  flag <- extra_params$fusions_left_match_flag
  if (!is.null(flag) && !flag) {
    return(handler_data)
  }
  if (!is.null(left_gene)) {
    index <- str_detect(handler_data[, gene_5], sprintf("^%s$", left_gene))
    return(handler_data[index, ])
  } else {
    return(handler_data)
  }
}

mhandler_fusions_right_match <- function(handler_data, config_input, extra_params = list(gene_3 = 2, 
  right_gene = NULL, fusions_right_match_flag = TRUE)) {
  right_gene <- extra_params$right_gene
  gene_3 <- extra_params$gene_3
  flag <- extra_params$fusions_right_match_flag
  if (!is.null(flag) && !flag) {
    return(handler_data)
  }
  if (!is.null(right_gene)) {
    index <- str_detect(handler_data[, gene_3], sprintf("^%s$", right_gene))
    return(handler_data[index, ])
  } else {
    return(handler_data)
  }
}

mhandler_fusions_any_match <- function(handler_data, config_input, extra_params = list(gene_5 = 1, 
  gene_3 = 2, any_gene = NULL, fusions_any_match_flag = TRUE)) {
  any_gene <- extra_params$any_gene
  gene_5 <- extra_params$gene_5
  gene_3 <- extra_params$gene_3
  flag <- extra_params$fusions_any_match_flag
  if (!is.null(flag) && !flag) {
    return(handler_data)
  }
  if (!is.null(any_gene)) {
    index_1 <- str_detect(handler_data[, gene_5], sprintf("^%s$", any_gene))
    index_2 <- str_detect(handler_data[, gene_3], sprintf("^%s$", any_gene))
    return(handler_data[index_1 | index_2, ])
  } else {
    return(handler_data)
  }
}

mhandler_fusions_full_match <- function(handler_data, config_input, extra_params = list(gene_5 = 1, 
  gene_3 = 2, left_gene = NULL, right_gene = NULL, fusions_full_match_flag = TRUE)) {
  left_gene <- extra_params$left_gene
  right_gene <- extra_params$right_gene
  flag <- extra_params$fusions_full_match_flag
  if (!is.null(flag) && !flag) {
    return(handler_data)
  }
  gene_5 <- extra_params$gene_5
  gene_3 <- extra_params$gene_3
  if (!is.null(left_gene) && !is.null(right_gene)) {
    index_1 <- str_detect(handler_data[, gene_5], sprintf("^%s$", left_gene))
    index_2 <- str_detect(handler_data[, gene_3], sprintf("^%s$", right_gene))
    return(handler_data[index_1 & index_2, ])
  } else {
    return(handler_data)
  }
}

mhandler_fusions_anyfull_match <- function(handler_data, config_input, extra_params = list(gene_5 = 1, 
  gene_3 = 2, left_gene = NULL, right_gene = NULL, fusions_anyfull_match_flag = TRUE)) {
  left_gene <- extra_params$left_gene
  right_gene <- extra_params$right_gene
  gene_5 <- extra_params$gene_5
  gene_3 <- extra_params$gene_3
  flag <- extra_params$fusions_anyfull_match_flag
  if (!is.null(flag) && !flag) {
    return(handler_data)
  }
  if (!is.null(left_gene) && !is.null(right_gene)) {
    index_1 <- str_detect(handler_data[, gene_5], sprintf("^%s$", left_gene))
    index_2 <- str_detect(handler_data[, gene_3], sprintf("^%s$", right_gene))
    
    index_3 <- str_detect(handler_data[, gene_5], sprintf("^%s$", right_gene))
    index_4 <- str_detect(handler_data[, gene_3], sprintf("^%s$", left_gene))
    return(handler_data[(index_1 & index_2) | (index_3 & index_4), ])
  } else {
    return(handler_data)
  }
}