FarzanehRah

Hi, thank you for your reply. Yes, I am using `bigFile=TRUE`. I applied the `shiftGAlignmentsList` function to one replicate of my samples. However, I encountered issues in the subsequent steps...

Actually, I have the results for one chromosome, but the researcher prefers to have information for the entire genome since the results are not interpretable in isolation, Thanks again. 

So, at which point should I merge them? For instance, to generate a `PTscore `plot of the entire genome, I require a gal1 object of all chromosomes. However, creating a...

Thank you so much. Regarding the `--resid-cutoff,` I was able to define the value successfully. However, I'm still encountering an issue even after setting `--sig-cutoff` to 1: `"m0 estimate for...

Thank you for your response. I'm curious if it would be possible to obtain some results by increasing the FDR threshold. Would that potentially yield some DMSs/DMRs? Additionally, I'm interested...

Thank you so much for your help.