threshold {betaclust}R Documentation

Thresholds under the K.. and the KN. models

Description

An objective method to calculate the threshold points for the clustering solution of the K.. and the KN. models.

Usage

threshold(object, data, model_name)

Arguments

object

A beta_k or beta_kn object.

data

A dataframe of dimension C \times NR containing methylation values for C CpG sites from R sample types collected from N patients which was passed as an argument to the betaclust function.

model_name

The name of the model for which the thresholds need to be calculated.

Details

As the K.. model constrains the shape parameters to be equal for all patients, a single pair of threshold points are calculated for all patients. The KN. model allows patient-specific shape parameters which results in a pair of threshold points for each patient based on the shape parameters for that patient. The first threshold point means that any CpG site with beta value less than this value is likely to be hypomethylated. The second threshold point means that any CpG site with beta value greater than this is highly likely to be hypermethylated. A CpG site with beta value lying between the two threshold points is likely to be hemimethylated.

Value

thresholds - The threshold points calculated for the selected model. A vector containing two threshold points are returned for the K.. model whereas a matrix containing two threshold points for each patient is returned for the KN. model.

See Also

beta_k

beta_kn

betaclust


[Package betaclust version 1.0.3 Index]