generateNAMfounders: Generate NAM founder genotypes

In behuang/spclust: Selective phenotyping for experimental crosses

Description

Generates founder genotypes for a Nested Association Mapping population

Usage

  generateNAMfounders(nparents, nmarkers, map, option = 1)

Arguments

nparents	Total number of parents
nmarkers	Number of markers on all chromosomes
map	Marker map
option	Process for generating genotypes. See details below.

Value

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).

Note

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.

behuang/spclust documentation built on May 12, 2019, 10:54 a.m.