getQuantiles: Return the percentiles of a betaMatrix for each probe type

In ARRmNormalization: Adaptive Robust Regression normalization for Illumina methylation data

Description

It returns the percentiles of a betaMatrix for Type I Green, Type I Red and Type II probes. If no list of probes is provided, all probes are taken into account to compute the percentiles.

Usage

getQuantiles(betaMatrix,goodProbes=NULL)

Arguments

betaMatrix	matrix containing the Beta values. Rows are probes, columns are samples.
goodProbes	Ids of the probes to be normalized (Id. of the form "cg00000029").

Value

Returns a list of three matrices of percentiles. For Type I green and Type I red probes, the corresponding matrices can be accessed by $green and $red. For Type II probes, the matrix can be accessed by $II

Author(s)

Jean-Philippe Fortin <[e-mail]>

Examples

data(greenControlMatrix)
data(redControlMatrix)
data(sampleNames)
data(betaMatrix)
quantiles=getQuantiles(betaMatrix)

ARRmNormalization documentation built on Nov. 8, 2020, 5:25 p.m.