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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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regional plot #39

Closed chenyangjjj closed 1 year ago

chenyangjjj commented 1 year ago

Hi,Yunye, I had a question about regional plot. As is shown is the below figure, I found that plot_mqq function will find lead variant (SNP X)automatically in this chunk of genome. But I am interested in another SNP(SNP Y) not the most significant one(SNP X). How should I set the parameters in plot_mqq(), and calculate its LD relation with other SNPs in selected region. I used to do it in Locuszoom.

image
Cloufield commented 1 year ago

Hi, you can use region_ref to change the reference variant.

For example, image

You can also use region_ref and region_ref2 to select two reference variants.

image

Cloufield commented 1 year ago

And please specify the genome build using build="19" or build="38".

chenyangjjj commented 1 year ago

Thank you! Yunye