fake.population: Simulate a population object.

In pheno2geno: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

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.

Details

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

Value

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

Author(s)

Konrad Zych [e-mail], Danny Arends [e-mail] Maintainer: Konrad Zych [e-mail]

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

	population <- fake.population()

pheno2geno documentation built on May 2, 2019, 6:35 a.m.