detectionP: Detection p-values

In hhhh5/ewastools: EWAS Tools

Detection p-values

Description

Compute detection p-values. p-values are based on the distribution of the intensities of the negative control probes or the U (M) intensities observed for completely methylated (unmethylated) probes, respectively (Heiss and Just, 2019). detP_threshold generates a plot showing the number of undetected Y chromosome probes among male and female subjects for various p-value thresholds, in order to empirically choose a threshold. Finally, mask is masking all probes with detection p-values below the specified threshold. detectionP.minfi provides an implementation for RGChannelSet objects as used in the minfi package.

Usage

summits(beta)

detectionP(raw)

detectionP.neg(raw)

mask(raw, threshold)

eval_detP_cutoffs(raw, males = NULL, females = NULL)

detectionP.minfi(rgSet)

Arguments

raw	Output of calling read_idats, must include component detP for mask and detP_threshold.
threshold	p-value threshold (arithmetic scale) above which oberservations are set to NA.
rgSet	minfi rgSet object
male/female	Indices of male and female subjects

Value

For detectionP and detectionP.neg a modified raw object with a detP component, a matrix of detection p-values, added. detectionP computes p-values on the linear scale, whereas detectionP.neg returns p-values on the log10 scale.

For detectionP.minfi a matrix of detection p-values.

For mask, a modified raw object, with undetected probes set to NA.

Vector of length two

Author(s)

Jonathan A. Heiss

References

Heiss JA, Just AC. Improved filtering of DNA methylation microarray data by detection p values and its impact on downstream analyses. Clinical Epigenetics (2019) 11:15 Return peaks of beta-value distribution

Return the locations of the two peaks (completly methylated and unmethylated CpG sites) of the beta-value distribution.

hhhh5/ewastools documentation built on Feb. 7, 2024, 6:21 p.m.