remove_batch_effect: Remove batch effect.
In markgene/yamat: Yet Another Methylation Array Toolkit

remove_batch_effect

R Documentation

Remove batch effect.

Description

Remove batch effect.

Usage

remove_batch_effect(
  x,
  batch = NULL,
  batch2 = NULL,
  method = c("mum", "cn", "beta"),
  offset = 1,
  verbose = TRUE,
  ...
)

Arguments

`x`	An object of `MethylSet-class` or `GenomicMethylSet-class` if `method` is "mum". An object of `RatioSet-class` or `GenomicRatioSet-class` if `method` is "cn" or "beta".
`batch`	A character scalar of the column name of interested batch in phenotype `data.frame`. Default to `NULL`.
`batch2`	A character scalar of the column name of interested batch2 in phenotype `data.frame`. Default to `NULL`.
`method`	A character scalar of methods, including "mum" (methylation and unmethylation separately), "cn" (copy number), "beta" (beta-value). Default to "mum".
`offset`	The offset is chosen to avoid log2 transform on zeros. Default to 1. Only valid for "mum" method.
`verbose`	A logical scalar. Default to TRUE.
`...`	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.