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How to get gene level H4? #87
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the overall PP for H4 is returned in summary
…On Fri, 2022-05-13 at 02:32 -0700, mhaiyue wrote:
Hi,
I am trying to run coloc.susie using GWAS summary statistics and GTEx
data.
GTEx data is grouped by gene, I'm testing each gene at one time.
I get SNP level H4 from the result, how do I get gene level H4?
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There are a lot of PP.H4.abf in usie.res$summary. How to interpret this coloc.susie results ?
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This means your first trait had 10 distinct credible sets in the susie results, and each line is the summary of colocalisation between each of these and the single signal found for the second trait. The first set appears to colocalise.
I should note that when susie has found 10 signals for me, it has normally identified an issue with the LD meaning that many of the signals are false. One (not foolproof) diagnostic is to look at the marginal p values for the identified snps.
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From: WB ***@***.***>
Sent: Wednesday, March 20, 2024 8:50 AM
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Subject: Re: [chr1swallace/coloc] How to get gene level H4? (Issue #87)
There are a lot of PP.H4.abf in usie.res$summary.
How to interpret this coloc.susie results ?
susie.res$summary
nsnps hit1 hit2 PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf idx1 idx2
1: 4591 rs12509595 rs1458038 0.000000e+00 4.147380e-13 0.000000e+00 0.02012341 9.798766e-01 1 1
2: 4591 rs10213506 rs1458038 1.570304e-273 1.878073e-11 8.361250e-263 1.00000000 6.399585e-12 2 1
3: 4591 rs74780855 rs1458038 5.954240e-106 1.878073e-11 3.170398e-95 1.00000000 1.328367e-13 3 1
4: 4591 rs72661739 rs1458038 1.556576e-79 1.878073e-11 8.288157e-69 1.00000000 1.963290e-13 4 1
5: 4591 rs10006582 rs1458038 1.476746e-59 1.878073e-11 7.863090e-49 1.00000000 6.277067e-13 5 1
6: 4591 rs6848130 rs1458038 2.330814e-86 1.878073e-11 1.241066e-75 1.00000000 2.036101e-09 6 1
7: 4591 rs2867702 rs1458038 1.508344e-52 1.878073e-11 8.031337e-42 1.00000000 3.088207e-13 7 1
8: 4591 rs10029510 rs1458038 6.966293e-45 1.878073e-11 3.709276e-34 1.00000000 1.354325e-12 8 1
9: 4591 rs7668598 rs1458038 1.734194e-52 1.878073e-11 9.233902e-42 1.00000000 1.516226e-12 9 1
10: 4591 rs1987331 rs1458038 1.352851e-41 1.878073e-11 7.203400e-31 1.00000000 3.023677e-13 10 1
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Thanks for the response. I didn't order the LD matrix for the SNPS previously. However, I reordered both SNPs of LD matrix and Snps of coloc$snp, and keep them in the same order. The ouput results are the same. Some of the p values for the identified snps are not significant. Here are the original P values:
1: 4 80674651 rs10006582 c g 0.740 -0.000779 0.0003916 4.683e-02 567207 79753497 trait 2 pQTL data from UKBppp
1: 4 79753497 rs10006582 4:80674651:C:G:imp:v1 G C -0.0139488 0.00816120 0.2625230 1.058380 |
Here is my coloc dataset. https://e.pcloud.link/publink/show?code=XZeNH9Zh05TXIv8uSBHQWEhApGjaSNGryXV |
Hi,
I am trying to run coloc.susie using GWAS summary statistics and GTEx data.
GTEx data is grouped by gene, I'm testing each gene at one time.
I get SNP level H4 from the result, how do I get gene level H4?
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