CNV.detail: CNV.detail

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

Description

Combine single probe values within detail regions.

Usage

CNV.detail(object, ...)

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

Arguments

object	CNV.analysis object.
...	Additional parameters (CNV.detail generic, currently not used).

Details

The median intensity per detail region is calculated. Detail regions are defined using CNV.create_anno(detail_bed=)

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.