dnacopy_analysis: Run DNAcopy analysis.

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

Description

Run DNAcopy analysis.

Usage

dnacopy_analysis(x, lrr, seed = 1, verbose = TRUE, ...)

Arguments

x	A minfi object such as RGChannelSet-class or MethylSet-class or GenomicMethylSet-class or GenomicRatioSet-class.
lrr	A matrix of log2 transformed ratio of query and reference copy number (sum of methylation and unmethylation signals).
seed	An integer scalar to set the seed. Default to 1.
verbose	A logical scalar. Default to TRUE.
...	Arugments passed to segment.

Details

The function provides a template of run DNAcopy analysis. There are many parameters in smoothing and segmentation. The function uses the default settings for smoothing.

Value

A list of two element:

• DNAcopy a DNAcopy object.

• CNA a codeCNA object (not smoothed).

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