R/error.check.R

In OmicsQC: Nominating Quality Control Outliers in Genomic Profiling Studies

#' Test if the zscore dataframe is correctly formatted. Raises and error if it is not.
#'
#' @param zscores The dataframe one wants to test
#' @noRd
zscore.format.check <- function(zscores) {

    # Numeric data frame
    dataframe.numeric <- all(apply(zscores, 2, is.numeric));

    if (!dataframe.numeric) {
        stop('dataframe is not fully numeric');
        }

    # Column names and row names
    if (is.null(rownames(zscores))) {
        stop('Please specify sample IDs by setting the rownames');
        }

    if (is.null(colnames(zscores))) {
        stop('Please specify metrics by setting the colnames');
        }

    # Missing data
    if (any(is.na(zscores))) {
        stop('Current version of OmicsQC does not support missing data');
        }

    return(NULL);
    }

#' Test if a dataframe is the valid output of accumulate.zscores
#'
#' @param quality.scores The dataframe one wants to test
#' @noRd
accumulate.zscores.output.check <- function(quality.scores) {

    stopifnot(is.data.frame(quality.scores))

    if (!('Sum' %in% colnames(quality.scores)) || !('Sample' %in% colnames(quality.scores))) {
        stop('quality.scores must be a data.frame that contains the columns Sum and Sample');
        }

    if (!is.numeric(quality.scores[,'Sum'])) {
        stop('The column Sum in quality.scores must be numeric');
        }

    if (!is.character(quality.scores[,'Sample']) && !is.factor(quality.scores[,'Sample'])) {
        stop('Sample ids must be character or factor');
        }

    if (length(quality.scores[,'Sample']) != length(unique(quality.scores[,'Sample']))) {
        stop('Sample ids must be unique');
        }

    return(NULL);
    }

#' Test if a trim.factor is valid
#'
#' @param trim.factor The trim.factor one wants to test
#' @noRd
check.valid.trim.factor <- function(trim.factor) {

    if (!is.numeric(trim.factor) || (trim.factor < 0) || (trim.factor > 0.5)) {
        stop('trim.factor must be a numeric in the range of [0, 0.5]');
        }

    return(NULL);
    }


#' Test if a alpha.significant is valid
#'
#' @param alpha.significant The alpha.significant one wants to test
#' @noRd
check.valid.alpha.significant <- function(alpha.significant) {

      if (!is.numeric(alpha.significant) || (alpha.significant < 0) || (alpha.significant > 1)) {
          stop('alpha.significant must be a numeric in the range of [0, 1]');
          }

      return(NULL);
      }

#' Test if a no.simulations is valid
#'
#' @param no.simulations The no.simulations one wants to test
#' @noRd
check.valid.no.simulations <- function(no.simulations) {

    if (!is.numeric(no.simulations) || !(no.simulations > 0)) {
        stop('no.simulations must be a positive number');
        }

    return(NULL);
    }