How to extract the position of the conserved DMCs

[Nsbaizan]

Hi, I would like to use your package for the analysis of RRBS data. First of all, do you think it is appropiate to use Mathylinheritance with RRBS data or should it be only fro WGBS? Can or should I make any fine-tuning for RRBS? Also, once the conserved DMCs are identified, how can I know the actual positions of the conserved DMCs? I manage to extract the results of each permutation but not the chromosome, start, end of each CpG that is conserved. Finally, I would like to ask if I can use this package with only 2 generations instead of 3. Thank you very much for your help!

[adeschen]

Hi Nsbaizan,

First, the methylInheritance package has been tested on RRBS data. The publication presenting the software uses a RRDS dataset as the biological example (see link below). So, it is totally appropriate to use with RRBS data.

Second, the software can be used on 2 generations instead of 3. However, the software has been developed with 3 generations in mind and might not have been tested thoroughly for 2.

Third, the conserved sites (or regions) are calculated through the runObservation() function. You can refer to the 6.2 section of the vignette: http://bioconductor.org/packages/release/bioc/vignettes/methylInheritance/inst/doc/methylInheritance.html

Finally, keep in mind that the total number of simulations needed to get a reliable statistic is high and can be time consuming.

The associated publication:
https://academic.oup.com/nar/article/46/14/e85/4994677

If you have other questions/problems, don't hesitate to ask.

Best,
Astrid