CNV.analysis-class: CNV.analysis class

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

Description

CNV analysis data of a single sample is stored in this class

Usage

## S4 method for signature 'CNV.analysis'
show(object)

## S4 method for signature 'CNV.analysis'
names(x)

## S4 replacement method for signature 'CNV.analysis'
names(x) <- value

## S4 method for signature 'CNV.analysis'
coef(object)

Arguments

object	CNV.analysis object
x	CNV.analysis object (defined by show generic).
value	Replacement names.

Details

Use CNV.fit to create. Modified by CNV.bin, CNV.detail and CNV.segment.

Value

CNV.analysis class.

Author(s)

Volker Hovestadt [e-mail]

Examples

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

# 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'

# output plots
CNV.genomeplot(x)
CNV.genomeplot(x, chr = 'chr6')
#CNV.detailplot(x, name = 'MYCN')
#CNV.detailplot_wrap(x)
CNV.write(x, what = 'segments')

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