Description Usage Arguments Value Note
Generates founder genotypes for a Nested Association Mapping population
1 | generateNAMfounders(nparents, nmarkers, map, option = 1)
|
nparents |
Total number of parents |
nmarkers |
Number of markers on all chromosomes |
map |
Marker map |
option |
Process for generating genotypes. See details below. |
A matrix with nparents rows and nmarkers columns, with values in 0, 1. The attribute "MAF" will give a vector containing minor allele frequencies for each marker (set at 1/nparents if option 1 is selected).
If option==1 (default), the common parent (1) is assumed to have a different value from all the other parents. This would be achieved if markers were chosen for which that parent had a rare allele. If option==2, then the minor allele frequency for each markers is uniformly distributed on [0, .5] and parents are randomly assigned one of two alleles (0 or 1) according to the allele frequency. Note that in all cases "1" is the minor allele. The marker map is currently only used for the marker names, but alternative methods of generating founder genotypes could depend on it. If it is not input a default marker naming will be used.
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