conumee_pipe: CNV pipeline based-upon Conumee package.
In markgene/yamatCN: Yet Another Methylation Array Toolkit Copy Number Analysis

Description Usage Arguments Details Value

CNV pipeline based-upon Conumee package.

conumee_pipe(ref, qry, report_dir, norm_method = c("swan", "illumina",
  "raw", "quantile", "noob", "funnorm", "yamat", "dkfz", "methylcnv"),
  batch = NULL, batch2 = NULL, batch_effect_method = c("cn", "mum",
  "beta"), pipe_file = "conumee.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, 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".
`pipe_file`	A character scalar of the filename storing the pipeline result sample by sample. Default to "conumee.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.
`...`	Any arguments passed to `CNV.segment`.

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 ConumeePipe class.

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