SampleHaplotype: Simulate a haplotype

Description

Simulates a haplotype, either sampling using population parameters or through a meiosis event with two parental haplotypes.

Usage

SampleHaplotype(H0 = NULL,H1 = NULL,genDist,nDec,nChrom = 1,prMut =
1E-5,QTL = F,checkValidity = TRUE)

Value

An object of class haplotype.

Arguments

H0: If specified, the first parental haplotype.
H1: If specified, the second parental haplotype. If neither H0 nor H1 are specified, a new haplotype is sampled from a base population. Errors message is displayed when only one haplotype is provided as meiosis occurs between two haplotypes.
genDist: Map size of the simulated genome in Morgan.
nDec: Number of decimals until which marker positions are rounded. Partially specifies marker density on the chromosome.
nChrom: Number of chromosomes, default at 1
prMut: Probability of marker bp mutation.
QTL: If TRUE, qtl alleles are inherited to the next generation. See function AssignQTL for assigning qtl to a list of haplotypes.
checkValidity: If TRUE, tests if a pair of haplotypes is compatible; e.g. if the number of traits in both is equal (or 0) and if the sizes are equal.

Details

Markers are continually spaced over the whole genome. Marker density is specified in SampleBaseHaplotype. Position of 1 alleles is recorded and stored in @snp attribute of the object of class haplotype. If QTL is TRUE, haplotypes with QTL's need to be provided. If not, nothing happens apart from mutations (same prob. as for single basepairs). Function SampleHaplotype is generally called by function SampleHaplotypes.

Examples

Run this code

hList <- SampleHaplotypes(nHaplotypes = 20,genDist =
1,nDec = 3,nLoc = 20) ## create objects
h <- SampleHaplotype(H0 = hList[[1]],H1 = hList[[2]],genDist =
1,nDec = 3)