forqs module reference
Forward simulation of Recombination, Quantitative traits, and Selection
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VariantIndicators

classes for specifying haplotype SNP values More...

Classes

class  VariantIndicator_Trivial
 trivial implementation: returns 0 More...
 
class  VariantIndicator_IDRange
 returns variant values based on specified haplotype id ranges and loci More...
 
class  VariantIndicator_IDSet
 flexible implementation: user specifies per-locus value and id list More...
 
class  VariantIndicator_Random
 Assigns SNP values randomly to individuals in the initial populations, independently for each locus with specified allele frequencies, so that each SNP will be in Hardy-Weinberg equilibrium (in expectation). More...
 
class  VariantIndicator_File
 returns variant values based on an ms-format file More...
 
class  VariantIndicator_SingleLocusHardyWeinberg
 Assigns SNP value 1 to both haplotypes of the first Np^2 individuals, and to one haplotype of the next N*2pq individuals. More...
 
class  VariantIndicator_TwoLocusLD
 Assigns SNP values according to allele frequencies at two loci and specified linkage disequilibrium (D). Note: all individuals are homozygotes, i.e. their haplotypes are identical. More...