cwob_pipe: CWOB pipeline.

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

Description

Conumee pipeline without binning.

Usage

cwob_pipe(ref, qry, report_dir, norm_method = c("swan", "methylcnv",
  "illumina", "raw", "quantile", "noob", "funnorm", "yamat", "dkfz"),
  batch = NULL, batch2 = NULL, pipe_file = "cwob.Rda",
  dnacopy_seed = 1, 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.
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 "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.
pipe_file	A character scalar of the filename storing the pipeline result sample by sample. Default to "cwob.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.

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 CwobPipe class.

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