assocComp {methylKit} | R Documentation |
This function associates principal components with sample annotations such as age, gender, batch_id. Can be used to detect which batch effects are associated with the variation in the methylation values.
assocComp(mBase, sampleAnnotation)
mBase |
|
sampleAnnotation |
a data frame where columns are different annotations and rows are the samples, in the same order as in the methylBase object. |
a named list of principal component matrix (named 'pcs'), by principal compopents (named 'vars') and a p-value matrix showing association p-values between sample annotations and principal components (named 'association').
Altuna Akalin
data(methylKit) sampleAnnotation=data.frame(batch_id=c("a","a","b","b"),age=c(19,34,23,40)) as=assocComp(mBase=methylBase.obj,sampleAnnotation)