search for: heterozyg

Sequenom has an odd format of calling a SNP genotype gg [1] "C" "GA" "A" "C" "C" "AG" "C" "C" "T" "G" homozygous A is called A and heterozygous is called AT The genetics package cannot handle the fact that some genotypes are declared with 2 letter while other are declared with only 1. Consequently the genotype() or makeGenotypes() will not work. I need to either find a clever way that the genetics package actually does do this. I think...

...ls are found in more than one sample, either they have survived into the next sampling at the same location, or have migrated to another another location and survived into the next sampling there. This pseudoreplication constitutes about 12% of all observations. I have information on the number of heterozygous locus per individual, its location, year, population size and number of immigrants at that location, and want to investigate the effect of population size and migration on heterozygosity through time. Heterozygosity, the response variable is a proportion, and I would like to account for the pse...

.... Here's the setup: the code below is part of a larger chunk that is calculating Fst values across loci and alleles. This chunk is designed to calculate the proportion ('p.a') of an allele ('a') at a locus in each population ('p') and the proportion of individuals heterozygous for that allele ('h.a'). I'm not concerned with being slick in terms of using the most convenient functions, but would rather have it do the calculations as fast as possible as this bit is getting run very frequently and seems to be taking the most compute time. Profiling seem...

...ages/poistweedie Simulation of models Poisson-Tweedie. * polysat (0.1) Lindsay V. Clark http://crantastic.org/packages/polysat polysat is a collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, and binary presence/absence formats. It can calculate pairwise differences between individuals using a stepwise mutation model or infinite alleles model. It can assist the u...