Question: methylation % calculation for targeted region
0
gravatar for prasundutta87
6 weeks ago by
prasundutta87360
prasundutta87360 wrote:

Hi,

I want to get the average methylation % for a targeted region, for example, see below...

Chrom   start   end Meth_%  count_methylated    count _unmethylated
chr1    1371409 1371409 0       0       5
chr1    1371539 1371539 0       0       88
chr1    1371567 1371567 2.32        2       84
chr1    1371572 1371572 2.30        2       85
chr1    1371575 1371575 1.12        1       88

The targeted region is chr1:1371409-1371575 and each row corresponds to a methylated C (1-based BEDgraph coverage file from bismark)

How should I proceed with my calculation?

1) Should I just take the mean of Meth % per locus? (Sum of Meth % values/5) i.e. (2.32+2.30+1.12)/5 or 1.148 %

OR

2) total count_methylated/total count_methylated+total count_unmethylated i.e. (2+2+1)/(2+2+1+5+88+84+85+88) = 0.014 or 1.4%

This one is more like a weighted mean (correct me if I am wrong).

OR

There is some other correct method to do this kind of calculation?

methylation • 118 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by prasundutta87360

Cross-posting in main GitHub for bismark page, hopefully, will get a reply there.

ADD REPLYlink written 6 weeks ago by prasundutta87360

Is your goal simply to represent this particular region? Or did you obtain it as a DMR (differentially methylated region) from some kind of analysis?

In the second case, I would represent (if you can) the same thing that the algorithm used. For example, the frequently used BSmooth pipeline does a weighted smoothing which takes into account coverage, so if I had used that algorithm, I would represent the smoothed values.

Another option is to set a coverage threshold (say >10 counts) and consider that all of the CpGs above the threshold have valid information. With that reasoning, I would not weigh the values. There are algorithms which work like this and do not take into account coverage when computing DMRs...

ADD REPLYlink written 6 weeks ago by Papyrus360

Hi,

Thanks for your reply. I just wanted to get methylation % as of now..but I have got a reply now..you can go to this link to find the answer, was meaning to post it anyway here: https://github.com/FelixKrueger/Bismark/issues/354

ADD REPLYlink written 6 weeks ago by prasundutta87360

thanks for the link, it's a great answer by Felix!

ADD REPLYlink written 6 weeks ago by Papyrus360
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1560 users visited in the last hour