dmrseq

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Error when running dmrseq function and question about generating PCA

3

Hello! First of all, thank you for this great package! I am running in to a problem when running the `dmrseq` function on ALL of my data. I have a...

amjass12

Changing y axis limits in plotDMRs

2

Thanks for this useful package, I was wondering if there is a way to override the ylim=(0,1) parameter in the plotDMRs function. I tried a nested function: `plot(plotDMRs(...), ylim=c(0,1))` but...

hernandezvargash

Duration of a permutation longer than previous one

3

Dear Keegan I am analyzing a WGBS dataset with dmrseq. The data is not human or mouse, so I used all the tips you gave here to figure out a...

tmms1

What are the suitable parameters for RRBS data?

6

Hi, In your paper you have mentioned that "dmrseq is generally applicable to WGBS data". My impression is that methods that work for WGBS also work for RRBS data. Have...

bishwaG

Regarding CPU usage: it will fill up the entire server’s CPU.

5

When I use dmrseq, I set BPPARAM = BiocParallel::MulticoreParam(workers = 2), but when I actually run it, this task occupies all the CPU of my server. How can I solve...

xuzhe010

Running block=TRUE crashes during permutations with "Error in .start_as_unnamed_integer(start)"

8

I am consistently getting the following error while running permutations. It doesn't always happen on the same permutation. Example output: Beginning permutation 1 ...Chromosome chr1: Smoothed (1.26 min). 38 CpG(s)...

mpiersonsmela

Loading samples in new R takes too long time

1

I use RStudio, and since I told that the best is to have the latest up-to-date version of the software I installed it, RStudio 2024 B 735 with R 4.4.1....

desmodus1984

Big FDR values for 42 sample

3

Hello, Thanks so much for this tool!!! I’m having some issues understanding why I’m getting such big FDR values, I’m currently working with 42 samples, 2 groups and 1000 permutations...

AndreaPeC

Rbind error during permutations

1

Hello! Thanks for the tool! I am encountering an error that seems to be recurrent but should have been fixed according to the forums. I am using dmrseq_1.26.0 , installed...

plbngl

Computing considerations for large data set

4

Hi Keegan, Hoping you can help shed some insight on my issue. I have 94 samples (emseq) in my dataset, and I am trying to run dmrseq with the test...

victoriaserelli