thank you. i will take a look claire,
Neil Shephard wrote: > > > > Claire_6700 wrote: >> >> Hello, >> >> I am having really hard time finding a good article about simulating >> genotypes of cases and controls at a disease locus using R. >> >> if you guys can point me or guide me where i can find more information, >> it will be helpful. >> >> > > The popgen() package allows the simulation of genotype data under a > coalescent model (via the treesim() function) or Multinomial-Drichlet > model (via the simMD() function). These won't quite simulate case-control > data, but can no doubt be tweaked to get two sets of data (cases and > controls) with the desired allele frequencies, LD etc. > > There is also the rmetasim() package which interfaces R with metasim. > > Alternatively if your after validation of p-values derived from genotypic > tests of association via simulation there is also the Direction Simulation > Approach (DSA) which is implemented in R > (http://www.mpipsykl.mpg.de/pages/english/research/mueller_downloads.htm). > > There is also an R plugin for plink > (http://pngu.mgh.harvard.edu/~purcell/plink/) which performs simulation of > unlinked loci that are in linkage equilibrium (although you may > specifically want to model linkage disequilibrium). > > And there is an R-plugin for PBAT which is for Population Based > Association Tests (http://people.fas.harvard.edu/~tjhoffm/pbatR.html). > > For other R-genetics information you may find the task-view at > http://cran.r-project.org/web/views/Genetics.html useful as well as > http://rgenetics.org/ > > There are also a host of other non-R options available though. Many under > the coalescent model (including one of the first by Richard Hudson, the ms > program) are linked from > http://en.wikipedia.org/wiki/Coalescent_theory#Software and additional > software for genetic analysis (including simulation in some instances) at > http://linkage.rockefeller.edu/soft/ . The vast majority will simply dump > output to text files, so its straight-forward to call them from within R > via a system call and then read the results into R. > > Neil > -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17071477.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.