Implementing covariates in calculating differential methylation
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3 months ago
Srinka ▴ 20

Could someone please assist me with the implementation of covariates in the calculateDiffMeth function?

I've been attempting to include parameters like age, BMI, and smoking status within a data frame while performing the calculation, but it keeps generating an error. The error message I'm encountering is,

two groups detected: will calculate methylation difference as the difference of treatment (group: 1) - control (group: 0) Error in data.frame(subst[, 1:4], tmp$p.value, p.adjusted(tmp$q.value, : arguments imply differing number of rows: 87001, 0, 1 In addition: Warning message: In mclapply(cntlist, logReg, vars, treatment = treatment, overdispersion = overdispersion, : all scheduled cores encountered errors in user code

Can anyone provide guidance on how to properly incorporate these covariates into the calculation process?

rrbs methylkit epigenomics • 171 views

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