champ.runCombat

A matrix of values representing the methylation scores for each sample (M or B). The default assumes you ran champ.norm and saved the output to "norm".

beta.c

This data.frame includes the information from the sample sheet. The default assumes you ran champ.load and saved the output to "myLoad".

If logitTrans=T then your data will be logit transformed before the Combat correction and inverse logit transformed after correction. This is T by default for Beta values but if you have selected M values it will revert to False. It is also False when used with CNA as those are intensity values that don't need to be transformed.
    	

logitTrans


This function formats data to run through ComBat batch correction. If beta values are used the data is first logit transformed. 


 ComBat 

The package includes quality control metrics, a selection
of normalization methods and novel methods to identify
differentially methylated regions and to highlight copy number
alterations. In addition there is a method to help calculate hmC using BS and oxBS samples.

Yuan Tian Tiffany Morris

ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

champ.runCombat function

If logitTrans=T then your data will be logit transformed before the Combat correction and inverse logit transformed after correction. This is T by default for Beta values but if you have selected M values it will revert to False. It is also False when used with CNA as those are intensity values that don't need to be transformed.

This function formats data to run through ComBat batch correction. If beta values are used the data is first logit transformed.

Function that uses ComBat to correct for batch effects related to slide/BeadChip.

The matrix of values represeting the methylation scores for each sample after ComBat batch correction.

champ.runCombat: Function that uses ComBat to correct for batch effects related to slide/BeadChip.

Description

Usage

Arguments

Value