pre_process_methylation: Preprocess the Beta value matrix

In whirlsyu/EnMCB: Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Preprocess the Beta value matrix

Description

This process is optional for the pipeline. This function pre-process the Beta matrix and transform the Beta value into M value.

Usage

pre_process_methylation(met,Mvalue,constant_offset,remove_na,remove_percentage)

Arguments

met	methylation matrix for CpGs. Rows are the CpG names, columns are samples.
Mvalue	Boolean value, TRUE for the M transformation.
constant_offset	the constant offset used in the M transformation formula.
remove_na	Boolean value, if TRUE ,CpGs with NA values will be removed.
remove_percentage	If precentage of NA value exceed the threshold(percentage), the whole CpG probe will be removed. Otherwise, the NA values are replaced with rowmeans.

Value

Object of class matrix.

Examples

demo_set<-create_demo()
pre_process_methylation(demo_set,Mvalue=FALSE)

whirlsyu/EnMCB documentation built on Jan. 25, 2023, 4:33 a.m.