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rhhao / csMR

Perform cell-stratified MR analysis through integrating GWAS and QTL data
GNU General Public License v3.0
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Question #1

Open Zhangzzzzzy opened 3 months ago

Zhangzzzzzy commented 3 months ago

I have a question, how do you choose the locus for co-localisation when co-locating? The original text says so: "We used default parameters to evaluate colocalization between GWAS signals and the expression of genes within 100 kb flanking regions." Does this default parameter include the delineation of motifs?

LockenLiu commented 3 months ago

Hi zhang,

  1. I'm not sure how to answer the first question, colocalization is used to find the locus(colocalizing SNPs), then those SNPs are filtered as instrumental variables in tow sample MR. As for settings of coloc, it is described in the Colocalization analyses, the Method part of our article.
  2. That description is related to the Fig.2d(expression of colocalized genes) and Fig.2e(LocusZoom plots of GWAS signals) in the article, used to show the expression of cell-specific colocalized genes and colocalized GWAS signals, so motifs may not be consider.