[PDF] Champ. NA mixte

What is Champ function?

Function provided by ChAMP to extract value from IDAT file, and mapping between CpGs and Probes on Chip. The older version of ChAMP used minfi to load data, this is a version provided by ChAMP. The function would read data from one directory, which contains IDAT files and phenotype data csv files.

Can I modify the internal structure of the result of Champ?

The internal structure of the result of champ.Block() function should not be modified if it’s not necessary caused it would be assigned as inpute for some other functions like Block.GUI(). You can try to use Block.GUI() to do interactively analysis on the result of champ.Block(). Yuan Tian

How do I use Champ DMR?

By default, we recommend user do champ.DMR on normalized beta value on two populations, like case to control. The function will return detected DMR and estimated p value. The three algorithms specified in this function is different, while Bumphunter and DMRcate calcuated averaged candidate bumps methylation value between case and control.

What's new in Champ DMP()?

New modification: champ.DMP() can now find numeric variable related CpGs, and do pairwise comparision between more than 2 phenotypes’ covariate. This function would use limma pack- age to calculate differential methylation probes between two phenotypes. Or use linear regression model to calcuate CpGs related with certain variables.