CNV.bin: CNV.bin

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

Description

Combine single probe intensitiy values into predefined bins.

Usage

CNV.bin(object, ...)

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

Arguments

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

Details

The median intensity per bin is calculated. Bins are defined using CNV.create_anno. A value by which all probe and bin intensity values are shifted in subsequent analysis steps is calculated by minimizing the median absolute deviation from all bins to zero (ideally shifting the copy-neutral state to 0).

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.