Hello all, I'm trying to calculate the Maximum likelihood of individuals to get the ancestry. I mixd 3 populations 15 generations in proportion of 20% 20% 60% when each population sorce have diferent genome (0 1 and 2) with frequencies for each one. So now i have individuals looks like 0 0 2 1 1 2 0 ..... and i don't now how to calculate the mle although i try to figure out from the package state4. can somebody help me please? Thanks [[alternative HTML version deleted]]
Erez Shabo <shaboerez <at> gmail.com> writes:> > Hello all, > > I'm trying to calculate the Maximum likelihood of individuals to get the > ancestry. > I mixd 3 populations 15 generations in proportion of 20% 20% 60% when each > population > sorce have diferent genome (0 1 and 2) with frequencies for each one. > So now i have individuals looks like 0 0 2 1 1 2 0 ..... and i don't now how > to calculate the > mle although i try to figure out from the package state4. > can somebody help me please?You haven't given quite enough information for us to help you. Remember that we're not all geneticists here ... can you give a little bit more context? Are you trying to estimate pedigrees, or populations of origin, or ... ? Another way to make it clearer would be to present the code you used to generate the "data" (it sounds like you did this in R). (The mle function from stats4 provides a *framework* for maximum-likelihood estimation; you still need to be able to write down a function for the likelihood of a given set of parameters.) Ben Bolker
Have you considered the Bioconductor project (www.bioconductor.org)? If you are not already familiar with their capabilities, I suggest you review their capabilities and consider posting a question to their listserve if you don't find the answer without that. hope this helps. spencer graves Erez Shabo wrote:> Hello all, > > I'm trying to calculate the Maximum likelihood of individuals to get the > ancestry. > I mixd 3 populations 15 generations in proportion of 20% 20% 60% when each > population > sorce have diferent genome (0 1 and 2) with frequencies for each one. > So now i have individuals looks like 0 0 2 1 1 2 0 ..... and i don't now how > to calculate the > mle although i try to figure out from the package state4. > can somebody help me please? > > Thanks > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html