Advise on adding peak height and variant coverage

[kwcurrin]

Hey Natsuhiko,

Thanks for developing PHM. We are excited to try it on our data.

I had a few questions regarding incorporating peak height and variant coverage by ATAC signal into the model. Specifically regarding the methods text from your paper:
"To compute ATAC-seq peak height, we pooled ATAC-seq data for the 100 samples. The peak height was defined as the highest value of the coverage depth within each peak region. Peak height was quantile normalised across all peaks. The relative coverage at each variant location (VL) was calculated by the absolute coverage depth divided by the peak height inside the peak. This value was used as the VL prior probability for both caQTL mapping and eQTL mapping. Peak distance was calculated based on the midpoint of a peak region."

questions:

1. As far as I can tell, the workflow in the README for PHM on github does not include code for incorporating peak height and variant coverage. Is this correct? If so, could you advise on how to incorporate these priors into the model? I can generate files of peak height and relative variant coverage based on your above methods text, but I am unsure how to convert these to files usable by PHM and in which steps they should be added.
2. Is distance between peaks handled by PHM internally using the peak annotation file? Or do we need to provide the distance between peaks?

Thanks!

Kevin