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chr1swallace / coloc

Repo for the R package coloc
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description errors #138

Open mocksu opened 8 months ago

mocksu commented 8 months ago

On the page https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html, there is a paragraph like this:

With these susie output objects stored, we can colocalise every pair of signals. This analysis says the first pair, tagged by s25.1 and s25 for datasets D3 and D4, do not colocalise (posterior for H3 is close to 1), whilst the second pair, tagged by the same SNP, s25, for both datasets, do (posterior for H4 is close to 1).

Which seems to be outdated and thus incorrect with the susie results:

##    nsnps hit1 hit2    PP.H0.abf    PP.H1.abf    PP.H2.abf    PP.H3.abf
## 1:   500 s105 s105 3.079008e-14 6.507291e-07 1.342030e-10 0.0008379729
## 2:   500  s89 s105 1.422896e-06 2.209787e-04 6.201896e-03 0.9631063075
##     PP.H4.abf idx1 idx2
## 1: 0.99916138    1    1
## 2: 0.03046939    2    1