Description Usage Arguments Details Value Author(s) See Also Examples

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

1 | ```
fixMethOutliers(object, K = -3, verbose = FALSE)
``` |

`object` |
An object of class |

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

`verbose` |
Should the function be verbose? |

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).

An object of the same class as `object`

where outlier values in
the methylation channels have been thresholded.

Rafael A. Irizarry and Kasper D. Hansen

1 2 3 | ```
if(require(minfiData)) {
MsetEx <- fixMethOutliers(MsetEx)
}
``` |

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