MrOlm
commented
1 week ago Hello,
Thank you for using inStrain and for your interest in exploring linkage relationships!
You can analyze the relationship between r² values for synonymous and nonsynonymous variants using the linkage output file generated by inStrain. Specifically, the linkage file contains information about pairwise linkage between variants, including r² values.
To extract the specific indicators you need:
Look for the variant_type column in the linkage file to identify synonymous and nonsynonymous variants. Filter the data to group r² values by their linkage type (e.g., synonymous-synonymous or nonsynonymous-nonsynonymous).
You can look at the code, here, that shows how we do then when making the linkage plots: https://github.com/MrOlm/inStrain/blob/master/inStrain/plotting/linkage_plots.py
Best, Matt
Hi, thank you for developing inStrain. Now i want to explore the relationship between r2 of synonymous variants linked to other synonymous variants and r2 of nonsynonymous variants linked to other nonsynonymous variants. How can i get these indicators in inStrain output files (maybe linkage file)?
Thanks in advance.