minfi (version 1.18.4)

detectionP: 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).

Value

A matrix with detection p-values.

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.

Examples

if (require(minfiData)) {

detP <- detectionP(RGsetEx)
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?

}