conumee_backbone: CNV pipeline backbone.

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

Description

CNV pipeline backbone is the steps after preprocessing, including loading data into Conumee, analysis and write the result.

Usage

conumee_backbone(x, report_dir, pipe_file = "conumee.Rda",
  dnacopy_seed = 1, overwrite = FALSE, verbose = TRUE, ...)

Arguments

x	An object of GenomicRatioSet-class or GenomicMethylSet-class.
report_dir	A character scalar of reporting.
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.

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 ConumeePipe class.

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