conumee (version 1.4.2)

CNV.segment: CNV.segment

Description

Segment bin values (wrapper of DNAcopy package).

Usage

CNV.segment(object, ...)
"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.

Value

CNV.analysis object.

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.

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'