preprocess: Preprocess

In markgene/yamatCN: Yet Another Methylation Array Toolkit Copy Number Analysis

Description

Preprocessing include normalization and batch effect removal.

Usage

preprocess(ref, qry, norm_method = c("swan", "illumina", "raw",
  "quantile", "noob", "funnorm", "yamat", "dkfz", "methylcnv"),
  batch = NULL, batch2 = NULL, batch_effect_method = "cn",
  overwrite = FALSE, verbose = TRUE)

Arguments

ref	Reference samples stored in an object of RGChannelSet-class.
qry	Query samples stored in an object of RGChannelSet-class.
norm_method	A character scalar of method, including raw, illumina, swan, quantile, noob, funnorm, yamat, dkfz, quantile, methylcnv. Default to "swan".
batch	factor or vector indicating batches. Default to NULL, - do not remove batch effect.
batch2	optional factor or vector indicating a second series of batches. Default to NULL, - do not remove batch effect.
batch_effect_method	A character scalar of methods, including "mum" (methylation and unmethylation separately), "cn" (copy number), "beta" (beta-value). Default to "cn".
overwrite	A logical scalar. Default to FALSE.
verbose	A logical scalar. Default to TRUE.

Details

The ref and qry should include at least the following columns Sample_Name, Gender, Batch, Sample_Prep. Batch effects are removed on methylation and unmethylation signals (log2 transformed) separately.

Value

An object of GenomicMethylSet-class or MethylSet-class. If norm_method is quantile, an object of GenomicRatioSet-class is returned.

markgene/yamatCN documentation built on Dec. 7, 2019, 4:36 a.m.