CNV.segment: CNV.segment

In conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Description

Segment bin values (wrapper of DNAcopy package).

Usage

CNV.segment(object, ...)

## S4 method for signature 'CNV.analysis'
CNV.segment(object, alpha = 0.001, nperm = 50000,
  min.width = 5, undo.splits = "sdundo", undo.SD = 2.2, verbose = 0,
  ...)

Arguments

object	CNV.analysis object.
...	Additional parameters supplied to the segment method of the DNAcopy package.
alpha	See details. Defaults to 0.001.
nperm	See details. Defaults to 50000.
min.width	See details. Defaults to 5.
undo.splits	See details. Defaults to 'sdundo'.
undo.SD	See details. Defaults to 2.2.
verbose	See details. Defaults to 0.

Details

This method is a wrapper of the CNA, segment, segments.summary and segments.p methods of the DNAcopy package. Please refer to the respective man pages for more detailed information. The default parameters of CNV.segment override some of the default parameters of segment and are optimized for 450k data CNV analysis.

Value

CNV.analysis object.

Author(s)

Volker Hovestadt [e-mail]

Examples

# prepare
library(minfiData)
data(MsetEx)
d <- CNV.load(MsetEx)
data(detail_regions)
anno <- CNV.create_anno(detail_regions = detail_regions)

# create object
x <- CNV.fit(query = d['GroupB_1'], ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno)

# modify object
x <- CNV.bin(x)
x <- CNV.detail(x)
x <- CNV.segment(x)

# general information
x
show(x)

# coefficients of linear regression
coef(x)

# show or replace sample name
names(x)
names(x) <- 'Sample 1'

conumee documentation built on Nov. 8, 2020, 6 p.m.