remove_batch_effect_mum: Remove batch effect: methylation and unmethylation signals.

In markgene/yamat: Yet Another Methylation Array Toolkit

Remove batch effect: methylation and unmethylation signals.

Description

Remove batch effect for methylation and unmethylation signals (log2 transformed) separately. See Capper D. DNA methylation-based classification of central nervous system tumours. Nature (2018).

Usage

remove_batch_effect_mum(x, batch = NULL, batch2 = NULL, offset = 1, ...)

Arguments

x	An object of MethylSet-class or GenomicMethylSet-class.
batch	factor or vector indicating batches.
batch2	optional factor or vector indicating a second series of batches.
offset	The offset is chosen to avoid log2 transform on zeros. Default to 1.
...	Other arguments can be passed to removeBatchEffect.

Details

Batch effect is removed by calling removeBatchEffect. The methylation and unmethylation signals are log2 transformed, removed batch effect, and transformed back.

Value

An object of argument x class.

markgene/yamat documentation built on Aug. 26, 2024, 11:56 p.m.