fixMethOutliers: Fix methylation outliers

Description

Methylation outliers (loci with very extreme values of the Meth or Unmeth channel) are identified and fixed (see details).

Usage

fixMethOutliers(object, K = -3, verbose = FALSE)

Arguments

object

An object of class [Genomic]MethylSet.

The number of standard deviations away from the median when defining the outlier cutoff, see details.

verbose

Should the function be verbose?

Value

An object of the same class as object where outlier values in the methylation channels have been thresholded.

Details

This function fixes outlying methylation calls in the Meth channel and Unmeth channel separately.

Unlike other types of arrays, all loci on a methylation array ought to measure something (apart from loci on the Y chromosome in a female sample). An outlier is a loci with a very low value in one of the two methylation channels. Typically, relatively few loci ought to be outliers.

An outlier is defined in a sample and methylation channel specific way. First the (sample, methylation channel) values are log2(x+0.5) transformed and then the median and mad of these values are computed. An outlier is then defined to be any value less than the median plus K times the mad, and these outlier values are thresholded at the cutoff (on the original scale).

Examples

Run this code

if(require(minfiData)) {
  MsetEx <- fixMethOutliers(MsetEx)
}