conumee (version 1.4.2)

CNV.bin: CNV.bin

Description

Combine single probe intensitiy values into predefined bins.

Usage

CNV.bin(object, ...)
"CNV.bin"(object)

Arguments

object

CNV.analysis object.

...

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

Value

CNV.analysis object.

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).

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'