8000 Eigenstrat for 3 subpopulations · Issue #66 · DReichLab/EIG · GitHub
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Eigenstrat for 3 subpopulations #66

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tahseen-igib opened this issue Jun 6, 2021 · 4 comments
Open

Eigenstrat for 3 subpopulations #66

tahseen-igib opened this issue Jun 6, 2021 · 4 comments

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@tahseen-igib
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Hi
I have a list of SNPs from 3 subpopulations pairwise association tests (1vs2 ,2vs3, 1vs3) that i need to 8000 check for population stratification.I have PC1-10 values for all the 3 subpopulations taken together.
However,in eigenstrat we have to define case-control to samples for chi-square test which in my case i have only for 2 subpopulations at a time.

Is it technically correct to take PC1-10 for 2 subgroups at a time and do the correction using eigenstrat?
Kindly suggest
@bumblenick
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bumblenick commented Jun 6, 2021 via email

@tahseen-igib
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Hi Nick

I have a deep phenotyped exome data that is subgrouped into 3 subpopulations based on some phenotypes.I am trying to understand genetic differences between those groups. Initially i have done PCA (using smartPCA) for complete population (all 3 groups included).
I have done aasociation test (fisher's exact test) by taking pair of groups at a time (1vs2,2vs3,1vs3).Each pairwise comparison has given me a list of significant SNPs.I want to filter out SNPs that have come due to population stratification and are not true signals.
For this i looked for Eigenstrat that will give chi-square corrected p value (correction for stratification by providing it PC components).& this needs our samples to be defined as case-control.
But in my case, i have got SNPs from paired group at a time & my PCs are representative of complete population (all 3 groups), my query is while doing eigenstrat for 1vs2 group SNPs (my case control will be 1 & 2 group) can i eliminate PCs from 3rd group??

I hope i am able to give u clear description of my problem

Thanks

@bumblenick
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bumblenick commented Jun 6, 2021 via email

@tahseen-igib
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Sure.I have sent u mail at nickp@broadinstitute.org.

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@bumblenick @tahseen-igib
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