Best way of visualising genetic variation for publication in a gene with many exons
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2.2 years ago
tacrolimus ▴ 140

Dear Biostars,

I have run "SAIGE-GENE" on a case control cohort genome wide. I have found an interesting gene and want to show the SNPs of interest across the gene in cases and controls.

There are 27 interesting SNPs in the cases (300 patients) and 400 SNPs in the controls. I have used the trackViewer package in R to create a lolliplop plot but the gene in question has 33 exons the graph is really compressed (image below). This is just in the cases! My question is:

a) Is there a way of only plotting exons on a lolliplop plot? b) has anyone got a better idea of how this data can be presented in a reader friendly manner?

All the best

enter image description here

graphs snv lollipop snp Visualisation • 342 views

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