coloc

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Hi, I'm using coloc for colocalization analysis between GWAS summary statistics and GTEx v8 eQTL data. I have a question that whether I should include all eQTL summaries or if...

TaoShiyue

Hi Chris, I hope this message finds you well. I am trying to run coloc.susie() for two datsets D1 and D2 and am having some trouble: - `D1_coloc_susie

char4816

Hi, I am very confused about the following output using coloc.susie(): nsnps hit1 hit2 PP.H0.abf PP.H1.abf PP.H2.abf 1: 406 chr17:snp1 chr17:snp2 2.073033e-20 1.746534e-16 1.121419e-06 2: 406 chr17:snp1 chr17:snp3 9.034574e-08 7.611643e-04...

catheriz

Hi, greetings! I would like to ask a question. I am running coloc for x=a GWAS summary data and y= a mQTL summary data. Now I get error: coloc error:...

forevertl

Hi, Thanks for creating this package. I tried to run colocalization with GWAS sumstats and mQTL data extracted from GoDMC dataset. However, there're some issues about the data structure to...

manL23

Results from coloc.abf

3

Hi, Thanks for developing the package, I am using coloc.abf and have run the following function: ``` coloc_abf_AL print(coloc_abf_AL$summary) nsnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 3.830000e+03 6.043220e-07 8.186484e-07 4.134895e-01 5.601097e-01...

Duhh56

For coloc, we have 5 competing hypotheses: H0: no causal variant H1: causal variant for trait 1 only H2: causal variant for trait 2 only H3: two distinct causal variants...

mocksu

Colocalization of eQTL and GWAS

5

Hi Chris, Thanks for making this fantastic package! I am working on the colocalization analysis with fine mapping using eQTL and GWAS. And I got some questions when I use...

cy6n

Interpretation on SNP.PP.H4

2

Hello, I am new to this amazing R package and just got confused about some outputs from the function coloc.abf(). I know that PP.H4 is the posterior probability of sharing...

zl2860

Using coloc for conditionally independent eQTLs in the HLA region

3

Hi Chris, Thanks for making this fantastic package! I had a conceptual question - I performed an eQTL analysis within the HLA region, and also did multiple rounds of conditional...

joycekang