detectionP {minfi} | R Documentation

## Detection p-values for all probed genomic positions.

### Description

This function identifies failed positions defined as both the methylated and unmethylated channel reporting background signal levels.

### Usage

    detectionP(rgSet, type = "m+u")

### Arguments

`rgSet` | An `RGChannelSet`.
`type` | How to calculate p-values. Only `m+u` is currently implemented (See details).

### Details

A detection p-value is returned for every genomic position in every sample. Small p-values indicate a good position. Positions with non-significant p-values (typically >0.01) should not be trusted.

The `m+u` method compares the total DNA signal (Methylated + Unmethylated) for each position to the background signal level. The background is estimated using negative control positions, assuming a normal distribution. Calculations are performed on the original (non-log) scale.

This function is different from the detection routine in Genome Studio.

### Value

A matrix with detection p-values.

### Author(s)

Martin Aryee aryee@jhu.edu.

### Examples

    if (require(minfiData)) {
      detP <- detectionP(RGsetEx.sub)
      failed <- detP>0.01
      colMeans(failed) # Fraction of failed positions per sample
      sum(rowMeans(failed)>0.5) # How many positions failed in >50% of samples?
    }

[Package minfi version 1.28.4 Index]