hypredFounder: Creates gametes of two founder lines
In timflutre/hypred: Simulation of Genomic Data in Applied Genetics

Description Usage Arguments Details Value See Also Examples

A generic function to create the gametes of two founder lines that differ at each locus, according to a defined genome.

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hypredFounder(object, ...)
## S4 method for signature 'hypredGenome'
hypredFounder(object, prob.snp)

`object`	an object of a class that holds information on a genome typically an `"hypredGenome"` object.
`prob.snp`	Numeric value that gives the probability that founder line 1 has the 1 allele at a locus.
`...`	Methods may require further arguments.

For each locus a 1 is sampled (using function sample) with probability prob.snp. Setting prob.snp = 1, results in gamete 1 having all the one alleles.

A two row matrix with as many columns as there are loci. Row 1 holds the gamete of line 1, row 2 the one of line 2. Row 2 is the exact negative of row 1 (i.e. if value[1, 1] == 1, than value[2, 1] == 0).

The function hypredGenome which creates the object, the function hypredNewMap which allows to modify the genetic map and the function hypredNewQTL which allows to assign QTL or modify already existing ones. The genome of the founders can be a starting point for the simulation of recombination using function hypredRecombine.

## one chromosome of length 1 M and 5 SNP

genome <- hypredGenome(1, 1.0, 5)

founders <- hypredFounder(genome,
                          prob.snp = 0.5) 

print(founders)