fixMethOutliers {minfi} | R Documentation

## 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`.
`K` | The number of standard deviations away from the median when defining the outlier cutoff, see details.
`verbose` | Should the function be verbose?

### 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).

### Value

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

### Author(s)

Rafael A. Irizarry and Kasper D. Hansen

### See Also

`minfiQC`

### Examples

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

[Package minfi version 1.40.0 Index]