hypred-package: hypred: Simulation of Genomic Data in Applied Genetics
In timflutre/hypred: Simulation of Genomic Data in Applied Genetics

Description Details Author(s)

The package hypred is intended for simulating high density genomic data. The meiosis is simulated under a count-location model, the genetic structure can include additive and dominance effects. The low level nature of the package provides great flexibility in creating all kinds of populations.

Package:	hypred
Type:	Package
Version:	0.5
Date:	2014-12-20
License:	GNU General Public License Version 2, June 1991
LazyLoad:	yes
Depends:	methods

The function hypredGenome is used to define the genome parameters, number and length of chromosomes, and number of SNP loci. It also simulates a genetic map. This functions returns an object that is of class hypredGenome. The function hypredNewMap is used to modify the genetic map, and the function hypredNewQTL to assign QTL. The function hypredFounder will create two homozygous founder lines according to the object returned by hypredGenome. The meiosis is simulated by the function hypredRecombine. This function takes two haploid chromosome sets (as found in a sex cell) and returnes a recombined haploid chromosome set (i.e. the gamete). The meiosis is simulated according to the count-location model, simulation of mutations is possible as well. The functions hypredTruePerformance and hypredTpGenomeSpecific return the true genotypic values of individuals given their genotypes. hypredTruePerformance uses the QTL effects found in the hypredGenome object, hypredTpGenomeSpecific allows to specify new and genome specific effects. Various types of design matrices (to be used in modeling algorithms) are created from the genotypes by the function hypredCode. All functions mentioned above are generic, with methods defined for the hypredGenome object.