Question: How To Keep Strand Information When Using Edmr Package To Analysis Data From Methylkit Package In R?
gravatar for dustar1986
6.0 years ago by
dustar1986300 wrote:


I'm using R packages to analysis my BS-sequencing data. I first used methylKit to find base-wise differential methylation. This result is with strand information for each base, looks like:

chr start end strand pvalue qvalue meth.diff

1 chr1 3000827 3000827 + 0.3666667 1 -9.090909

2 chr1 3000828 3000828 - 0.3264993 1 -8.029690


Then I applied eDMR to this data to find differential methylated region. But in the result, the strand information is all replaced with "*".

Is there a way to keep strand information?

Thanks in advance.

R • 1.7k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by dustar1986300

I am not sure (i don't use this library), but it might be that your data frame or the function call is not right. By quick google through their code and here it seems like they may "doctor" or de-strand your data if it doesn't meet their expectation.

ADD REPLYlink written 6.0 years ago by Pavel Senin1.9k

Thanks for these lots of reading Pavel. However, what you showed is the code of MethylKit. I did not lose the strand info at methylKit stage. Strand was lost in the following step using eDMR package. I've also checked its code but cannot find where they replace the strand with "*". Thank you again all the same.

ADD REPLYlink written 6.0 years ago by dustar1986300
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