R/filter_missing_values.R

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

    #' filter_missing_values
    #' @title Drop the Missing Values Above a Certain Threshold
    #' @param x A numeric matrix as input.
    #' @param max_miss_rate Maximal missing rate allowed for a feature;default
    #' is 20.
    #' @return A dataframe with features with missingness rate of more than
    #' user-defined threshold.
    #' @author Matineh Rahmatbakhsh, \email{matinerb.94@gmail.com}
    #' @description Given an input matrix, compute the missingness rate for
    #' each features and keep only features with missing rate more than
    #' user-defined percentage.
    #' @export
    #' @examples
    #' x <- matrix(1:10, ncol = 2)
    #' x[, 2] <- NA
    #' filter_missing_values(x, 30)
    filter_missing_values <-
      function(x, max_miss_rate = 20) {
        if (is.matrix(x)) x <- as.data.frame(x)
        if (missing(max_miss_rate)) {
          stop("Must provide percentage value for features removal")
        }
        if (length(colnames(x)) == 0) {
          stop("Column (feature) names are missing...")
        }

        # remove column with more than 20% missing values
        miss_prec <-
          colSums(is.na(x)) / nrow(x) * 100
        print(miss_prec[miss_prec > 20])
        col_miss <-
          names(miss_prec[miss_prec > 20])

        if (length(col_miss) == 0) {
          x
        } else {

          # Removing the columns with more than 20% missing value
          x[, c(col_miss)] <- NULL
        }
        return(x)
      }