normalize.methylcnv: Normalization MethylCNV.
In markgene/yamat: Yet Another Methylation Array Toolkit

normalize.methylcnv

R Documentation

Normalization MethylCNV.

Description

Normalization method used in MethylCNV pipeline, which adjust the median of log2 copy number on each array to a target value of 13.

Usage

normalize.methylcnv(rgset, target_value = 13, offset = 1)

Arguments

`rgset`	An object of `RGChannelSet-class`.
`target_value`	A numeric value to which the median of log2 copy number on each array is adjusted. Default to 13.
`offset`	A numeric scalar. It is only applicable when log2 transform is carried out. Default to 1.

Details

The method was used in copy number variant pipeline described in the paper Feng, G. A Statistical Method to Estimate DNA Copy Number from Illumina High-Density Methylation Arrays. Systems Biomedicine (2013). It adjust the median of log2 copy number on each array to a target value of 13.