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3 votes
Accepted

Population Allele Frequency

I don't know specifically about the UKBB RAP, however, Population Allele Count is the count of that specific allele genotyped in the population in question. In this case, it most likely refers to the ...
Yossi Farjoun's user avatar
2 votes

Is there any book or reference that explains evolutionary dynamics and fixation probability?

I'm fond of Joe Felsenstein's book on evolutionary genetics as a relatively recent source that presents a lot of these problems at a very simple level for the newer student, and then adds complexity ...
Maximilian Press's user avatar
2 votes

Is there any book or reference that explains evolutionary dynamics and fixation probability?

Maynard Smith, J. (1989) Evolutionary Genetics. Oxford: Oxford University Press. ISBN 0-19-850231-1 Maynard Smith, J. and Harper, D. (2003) Animal Signals. Oxford University Press. ISBN 0-19-852685-7[...
M__'s user avatar
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2 votes

How to compute Shanon entropy

I think there needs to be clarification of the question. Shannon entropy is not the same thing as the Shannon-Wiener diversity index (H), commonly referred to as the Shannon index. The reason I ...
M__'s user avatar
  • 12.5k
1 vote
Accepted

Confidence intervals around Q-matrix values from multiple STRUCTURE runs

If we consult the structure docs, we observe that they directly address the idea of a $Q$ distribution for each individual (p. 24), in the form of a Bayesian credible interval, which can be obtained ...
Maximilian Press's user avatar
1 vote

Predict population based on PC coordinates

Here is a very simple way to get your started. Of course you can make it more complex: Take the mean PC1 and PC2 coordinates for each 'reference panel population label' and then calculate the ...
user438383's user avatar
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1 vote

Predict population based on PC coordinates

I apologise for being negative about this, but I am afraid you cannot use principle components for population inference other than assigning clusters within a bivariate or 3D graph. Eigen values are ...
M__'s user avatar
  • 12.5k
1 vote

How to interpret Mendelian randomization results?

It looks like you have linkage as opposed to linkage disequilibrium, therefore horizontal pleiotropy is an explanation of the calculation. The calculation appears to be a GLMM around the beta ...
M__'s user avatar
  • 12.5k

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