Katarzyna Wreczycka
Katarzyna Wreczycka
hi @yplee614 and @alexg9010 , Sorry, I don't have a function for that. What I would do is: - convert your methylDiff object to GRanges `your.granges.object=as(yourmethdiffobject, "GRanges")` - use `reduce`...
I improved the code according to your suggestions besides @al2na suggestion about the if clause https://github.com/al2na/methylKit/pull/120#discussion-diff-199020615R31
@al2na I added more comments, hope it's better now
there is something wrong when `join.neighbours=TRUE` and `initialize.on.subset!=1`, I am checking it
I checked if with methylRawDB and multiple cores is faster than using methylRaw object on example of data with ~350K Cs (two chromosomes) and methylRaw is faster. I don't know...
I checked it using 5 chromosomes and it's not better. ``` > myRaw methylRaw object with 3784497 rows -------------- chr start end strand coverage numCs numTs 1 chr21 9411552 9411552...
@al2na @alexg9010 I didn't manage to show that this method is faster. Should we close this pull request?
Hi @balwierz , Ok, I see from where your error comes from, but if I remember correctly, @al2na and @frenkiboy implemented `constrainRanges` with `type="within"` argument to prevent windows outside of...
Hi balwierz, Could you create pull request with this feature, provide an example in vignette and write a test for it? Kasia
Hi @Julian-jly , what version of genomation are you using? I just quickly checked your code, and for me, it works just fine. Do you use S4Vectors package version >=...