Closed SophieValk closed 7 months ago
Hi Sophie,
Thanks for using methylKit!
Unfortunately I was not able to inspect the plots that you uploaded, it seems that the files are empty.
Best,
Alex
Hi @alexg9010 ,
Thankyou for taking the time to look at my issue. I figured out what was the problem. I did not correctly transform my CpG called .bed files into the required format for methylKit. The freqC and freqT did not add up together. Now that I fixed that the %methylation reaches 100%, also after uniting multiple documents.
Thanks again for providing methylKit, I will happily continue using it. This issue can be closed.
Best, Sophie
Hi Sophie, Thanks for letting us know.
Hi there,
Thankyou for providing the Methylkit package, I have really enjoyed using it so far.
I am trying to use MethylKit for identifying differences in DNA Methylation between two groups. After having imported all the sample files independently, I have checked their methylation profiles using the get MethylationStats function. All histograms show varying methylation ranging from 0% - 100%:![100pMethylation](https://github.com/al2na/methylKit/assets/106058726/c66aad31-f89e-428f-b4d7-e68120d84968)
$meth <- unite(myobj, destrand=TRUE) $head(meth)
When I then try to unite my samples, methylkit returns a methylBase object where the methylation percentage of all samples only reach until 50%. Regardless if I set the destrand option at TRUE or FALSE.
$PercMethylation <- percMethylation(meth) $View(PercMethylation)![Screenshot_percMethylation](https://github.com/al2na/methylKit/assets/106058726/3acab312-27ee-4015-856a-a5a54a603b28)
Am I doing something wrong or am I overseeing something? It seems that somehow in the unite function, the data gets divided by 2. I thought this may have something to do with the destrand option in unite but that did not seem to make a difference.
When I use destrand=FALSE, I get the following results with the following code: $meth <- unite(myobj, destrand=FALSE $PercMethylation <- percMethylation(meth) $View(PercMethylation)
I hope someone can explain what I might be doing wrong. Thanks, Sophie