detectionP: Detection p-values for all probed genomic positions.
In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

detectionP

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?
}

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.