search

al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
210 stars 96 forks source link

Which parameter determined the p value and q value but doesn't change the meth.diff ? #285

Closed DengEr-1993 closed 1 year ago

DengEr-1993 commented 1 year ago

Hello @alexg9010 ,

I have a small question about the calculateDiffMeth() function.

I can get different results if I use different parameters in calculateDiffMeth()

but I want to know if any parameters can only change the p value and q value but will not affect the meth.diff result ?

For exmaple, based on the scripts below, respectively :

myDiff_new = calculateDiffMeth(meth_new, overdispersion="MN", test="Chisq", num.cores = 10) or myDiff_new = calculateDiffMeth(meth_new, covariates = covariates, overdispersion="MN", test="Chisq", num.cores = 10)

how can I use other different paramters to change p value and q value but will not affect the meth.diff result of each line ?

I have confirmed that parameter "test=()" can change both values. Can adjust=() does it ?

Best, Xiangyi

alexg9010 commented 1 year ago

Hi @DengEr-1993,

Yes, correct. To modify the outcome of the p-value adjustment (q-value), simply change the adjust parameter of the calculateDiffMeth function. This should allow you to fine-tune the results and not change the reported methylation difference.

Best, Alex