agreement: Function to measure intra-replicate agreement for methylation...

In GreenwoodLab/funtooNorm: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

Function to measure intra-replicate agreement for methylation data.

Description

Function to measure intra-replicate agreement for methylation data.

Usage

agreement(Beta, individualID)

Arguments

Beta	: Matrix with beta-values, rows corresponding to probes, columns corresponding to samples.
individualID	: a vector where 2 replicates have the exact same value for two technical replicates. Order of samples should nmatch the samples (columns) in Beta

Details

We expect that the values returned by the agreement function after normalization by funtooNorm to be smaller than before.

Value

The average value of the square distance between replicates: a measure of agreement between replicates in methylation data.

Examples

agreement(cbind(rnorm(n = 10),rnorm(n = 10),rnorm(n = 10)),c(1,1,1))

GreenwoodLab/funtooNorm documentation built on April 5, 2022, 3:22 p.m.