Lep-MAP2 calculates sex-averaged positions using EM-type algorithm by restricting the two positions to be exactly same. This can yield different positions than averaging the two positions. You can average the male and female positions if that seems more appropriate.
Cheers,
Pasi
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Dear Pasi,
I was wondering how Lepmap2 computes sex averaged map?
For the following positions (male and female positions):
3.096 4.768
I would obtain ((3.096+4.768)/2)=3.932 as the sex averaged position
However, Lepmap2 gives 5.146 as the sex averaged. This is true for other positions as well. How is it then calculated?
Thank you,
Homa
Dear Homa,
Thank you for your question.
Lep-MAP2 calculates sex-averaged positions using EM-type algorithm by restricting the two positions to be exactly same. This can yield different positions than averaging the two positions. You can average the male and female positions if that seems more appropriate.
Cheers,
Pasi
Dear Pasi,
Thank you very much for your response.
Could you please explain a bit more what it means that it restricts the two positions to be exactly the same? In what regard they should be the same?
Thanks,
Cheers,
Homa
Dear Homa,
The hidden Markov model parameters in the EM algorithm are restricted to be same so that the two map positions become exactly the same.
Cheers,
Pasi