R/transform_raw.R

In proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

#' Functions to log transform raw data before normalization and batch correction
#' 
#' @inheritParams proBatch
#' @param log_base base of the logarithm for transformation
#' @param offset small positive number to prevent 0 conversion to \code{-Inf}
#' 
#' @return `log_transform_df()` returns \code{df_long}-size data frame, with 
#' \code{measure_col} log transformed; with old value in another column 
#' called "beforeLog_intensity" if "intensity" was the value of 
#' \code{measure_col};
#' `log_transform_dm()` returns \code{data_matrix} format matrix
#' 
#' @examples 
#' log_transformed_df <- log_transform_df(example_proteome)
#' 
#' log_transformed_matrix <- log_transform_dm(example_proteome_matrix, 
#' log_base = 10, offset = 1)
#' @name transform_raw_data
NULL

#' Log transformation of the data
#' 
#' @export
#' @rdname transform_raw_data
#'
log_transform_df <- function(df_long, log_base = 2, offset = 1,
                             measure_col = 'Intensity'){
  if(!is.null(log_base)){
    df_long = df_long %>%
      mutate(!!(paste('beforeLog', measure_col, sep = '_')) := 
               !!(sym(measure_col))) %>%
      mutate(!!(sym(measure_col)) := 
               log(!!(sym(measure_col)) + offset, base = log_base))
  } else {
    warning("Log base is NULL, returning the original data frame")
  }
  return(df_long)
}

#' "Unlog" transformation of the data to pre-log form (for quantification, forcing log-transform)
#' 
#' @export
#' @rdname transform_raw_data
#'
unlog_df <- function(df_long, log_base = 2, offset = 1, 
                     measure_col = 'Intensity'){
  if(!is.null(log_base)){
    df_long = df_long %>%
      mutate(!!(paste('beforeUnLog', measure_col, sep = '_')) := 
               !!(sym(measure_col))) %>%
      mutate(!!(sym(measure_col)) := 
               log_base^(!!(sym(measure_col)) - offset))
  } else {
    warning("Log base is NULL, returning the original data frame")
  }
  return(df_long)
}

#' 
#' @export
#' @rdname transform_raw_data
#'
log_transform_dm <- function(data_matrix, log_base = 2, offset = 1){
  if(!is.null(log_base)){
    data_matrix_log = log(data_matrix + offset, base = log_base)
  } else {
    warning("Log base is NULL, returning the original data matrix")
    data_matrix_log = data_matrix
  }
  return(data_matrix_log)
}

#' 
#' @export
#' @rdname transform_raw_data
#'
unlog_dm <- function(data_matrix, log_base = 2, offset = 1){
  if(!is.null(log_base)){
    data_matrix_unlog = log_base^(data_matrix) - offset
  } else {
    warning("Log base is NULL, returning the original data matrix")
    data_matrix_unlog = data_matrix
  }
  return(data_matrix_unlog)
}