R/replace_missing_data.R

In fosterlab/PrInCE-R: Predicting Interactomes from Co-Elution

#' Replace missing data with median ± random noise 
#' 
#' Replace missing data within each numeric column of a data frame with 
#' the column median, plus or minus some random noise, in order to train 
#' classifiers that do not easily ignore missing data (e.g. random forests or
#' support vector machines).
#' 
#' @param dat the data frame to replace missing data in 
#' @param noise_pct the standard deviation of the random normal 
#' distribution from which to draw added noise, expressed as a 
#' percentage of the standard deviation of the non-missing values in each 
#' column
#' 
#' @return a data frame with missing values in each numeric column replaced
#' by the column median, plus or minus some random noise
#' 
#' @importFrom stats rnorm
#' 
#' @export
replace_missing_data <- function(dat, noise_pct = 0.05) {
  for (col_name in colnames(dat)) {
    column <- dat[[col_name]]
    if (!is.numeric(column))
      next
    ## first, replace infinite values
    infinite = is.infinite(column)
    column[infinite] <- NA
    ## second, replace other missing values
    missing <- !is.finite(column)
    dat[[col_name]][missing] <- 
      median(column, na.rm = TRUE) + rnorm(sum(missing)) * 
      sd(column, na.rm = TRUE) * noise_pct 
  }
  return(dat)
}