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olive8306
•
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@olive8306-23019
Last seen 4.5 years ago
Hi,
I read the the source code of champ.DMR, I find the words:
X <- cbind(1,(as.numeric(as.factor(pheno))-1))
print(nrow(x))
Beta <- beta[bumphunter.idx,]
Beta <- replace(Beta,which(Beta <= 0.001),0.001)
Beta <- replace(Beta,which(Beta >= 0.999),0.999)
Y <- log((Beta/(1-Beta)),2)
Bumps <- bumphunter(Y,
design=X,
chr=Anno[bumphunter.idx,]$chr,
......
Does the DMR not still support the multi-phenotypes with the "bumphunter" method ? And I could not also find the compare.groups setting here. Do anyone know that? Thank!
the version of ChAMP is 2.16.1
Best,
Lei