conumee (version 1.4.2)

CNV.detail: CNV.detail

Description

Combine single probe values within detail regions.

Usage

CNV.detail(object, ...)
"CNV.detail"(object)

Arguments

object

CNV.analysis object.

...

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

Value

CNV.analysis object.

Details

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

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'