Question based on the calculation to covert bam file methylation values into beta values

[AzlanNI]

Hello everyone,

I am currently thinking about to use Bam2pat to convert some .bam files into .beta files.

I am using ONT .bam files and was just asking myself how the exact calculation looks like to convert the read based information from the .bam files to beta-values.

It would be great to understand the procedure before i start using it.

Thanks a lot!

kind regards, Azlan

[yonniejon]

Hi,

according to the docs directory of this package:

the beta file has: for each of the NR_SITES CpG sites in the genome, it holds 2 values: the #meth and #covered. Meaning, the i'th row in the matrix corresponds to the i'th CpG site:

#meth: the number of times the i'th site (CpGi) site is observed in a methylated state.
#coverage: the total number of times i'th site (CpGi) is observed. #coverage==0 is equivalent to a missing value (NaN).

CpGi's beta value is obtained by dividing #meth / #coverage.

Does that answer your question?

[AzlanNI]

Hello @yonniejon,

Thanks a lot for ur reply.

Alright so the beta values in the .beta file are calculated by using the the #Methylated reads / total reads for each CpG.

i got confused with the beta values calculation for the array based methylation analysis.

Thank you again!

Kind regards,

Azlan

[yonniejon]

Just to be clear - the beta file contains values for each row i: #Methylated reads with CpG i methylated, # reads covering CpG i

The calculation of "#Methylated reads / total reads for each CpG" you can do yourself by opening the beta file and taking the first value of the row and dividing by the second.

[AzlanNI]

Oh alright. I thought it was like the beta files from arrays. Where u have a beta value for each CpG in a matrix form.

But if the Beta File contains the methylation count and read count then i can just calculate it myself.

Thanks a lot!