pheno2geno (version 1.4.0)

fake.population: Simulate a population object.

Description

Simulates a basic population object for use in examples.

Usage

fake.population(n.founders = 4, n.offspring = 100, n.markers=100,n.chromosomes=10,
    type = c("riself", "f2", "bc", "risib"), n.mixups=0, verbose=FALSE,...)

Arguments

n.founders

Number of founders to be simulated.

n.offspring

Number of offspring individuals to be simulated.

n.markers

Number of markers individuals to be simulated.

n.chromosomes

Number of chromosomes individuals to be simulated.

type

Type of the cross to be faked:

• riself - RILs by selfing.

• f2 - f2 cross.

• bc - back cross.

• risib - RILs by sibling mating.

n.mixups

Number of mixups to be faked.

verbose

Be verbose.

...

To be passed to sim.cross.

Value

An object of class population. See create.population for details.

Details

This function simulates a population object that can be used for further analysis.

References

Copenhaver, G. P., Housworth, E. A. and Stahl, F. W. (2002) Crossover interference in arabidopsis. Genetics 160, 1631--1639.

Foss, E., Lande, R., Stahl, F. W. and Steinberg, C. M. (1993) Chiasma interference as a function of genetic distance. Genetics 133, 681--691.

Zhao, H., Speed, T. P. and McPeek, M. S. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics 139, 1045--1056.

Broman, K. W. (2005) The genomes of recombinant inbred lines Genetics 169, 1133--1146.

Teuscher, F. and Broman, K. W. (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175, 1267--1274.

See Also

• read.population - Load genotype, phenotype, genetic map data files into R environment into a population object.

• add.to.population - Add data to existing population object.

• sim.cross - Function from R/qtl package used to simulate genotypic data.

• create.population - Create object of class population from data already in R environment.

Examples

# NOT RUN {
	population <- fake.population()
# }