methylcnv_pipe: MethylCNV pipeline.
In markgene/yamatCN: Yet Another Methylation Array Toolkit Copy Number Analysis

Description Usage Arguments Details Value Note

The method was described in the paper Feng, G. A Statistical Method to Estimate DNA Copy Number from Illumina High-Density Methylation Arrays. Systems Biomedicine (2013).

methylcnv_pipe(ref, qry, report_dir, norm_method = c("methylcnv", "swan",
  "illumina", "raw", "quantile", "noob", "funnorm", "yamat", "dkfz"),
  batch = NULL, batch2 = NULL, pipe_file = "methylCNV.Rda",
  dnacopy_seed = 1, overwrite = FALSE, verbose = TRUE)

`ref`	Reference samples stored in an object of `RGChannelSet-class`.
`qry`	Query samples stored in an object of `RGChannelSet-class`.
`report_dir`	A character scalar of reporting.
`norm_method`	A character scalar of method, including raw, illumina, swan, quantile, noob, funnorm, yamat, dkfz, methylcnv. Default to "methylcnv".
`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.
`pipe_file`	A character scalar of the filename storing the pipeline result sample by sample. Default to "methylCNV.Rda". Turn off the saving by set it to NULL.
`dnacopy_seed`	An integer scalar to set the seed. Default to 1.
`overwrite`	A logical scalar. Default to FALSE.
`verbose`	A logical scalar. Default to TRUE.

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.

An object of CMethylCNVPipe class.

The method was named methylCNV according to Feng's paper. It is supposed to be implemented in the Lumi package. However, I did not find it by searching the name or CNV in its manual.

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