detectionP {minfi} | R Documentation |
This function identifies failed positions defined as both the methylated and unmethylated channel reporting background signal levels.
detectionP(rgSet, type = "m+u")
rgSet |
An |
type |
How to calculate p-values. Only |
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.
A matrix with detection p-values.
Martin Aryee aryee@jhu.edu.
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? }