hypredGenome-class: Class "hypredGenome"

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

Description

A class to hold information and data describing a genome in the context of high density SNP data.

Objects from the Class

Objects are created by the function hypredGenome or by calls of the form new("hypredGenome", ...)

Slots

num.chr:

Object of class "integer", giving the number of chromosomes.

len.chr:

Object of class "numeric", giving the length of the chromosomes (a vector with one entry for each chromosome.)

num.snp.chr:

Object of class "integer", giving the number of SNP marker per chromosome

pos.snp:

Object of class "numeric", giving the map positions (in M) of each loci (SNP marker and QTL). This is one vector. The loci from chromosome 1 come first, then the ones from chromosome 2 and so on. If there are 100 loci per chromosome, then elements 1:100 give the map of chromosome 1, 101:200 the map of chromosome 2 and so on.

pos.snp.block:

Object of class "numeric" giving the map positions (in M) of each loci (SNP marker and QTL). This is one vector. The loci from chromosome 1 come first, then the one from chromosome 2 and so on. If there are 100 loci per chromosome, then elements 1:100 give the map of chromosome 1, 101:200 the map of chromosome 2 and so on. In contrast to pos.snp, not all loci have distinct map positions. The map positions of all loci within one block of loci are identical.

block.info:

Object of class "list" holding information about the mentioned blocks. There should be three elements in this list: center, an integer vector giving the loci that are in the center of the blocks; end, an integer vector giving the loci that are at the end of the blocks; num.blocks.chr, an integer value giving the number of such blocks on each chromosome.

chr.break.pts:

Object of class "matrix". This is a two column matrix with as many rows as there are chromosomes that gives the ID of the first and last loci on a chromosome for vectors such as pos.snp. Chromosome 1 in row 1, chromosome 2 in row 2 and so on.

num.add.qtl.chr:

Object of class "integer". A single value that gives the number of QTL with additive effect on each chromosome (since all QTL must have an additve effect, this is identical to the number of QTL in general).

num.dom.qtl.chr:

Object of class "integer". A single value that gives the number of QTL with a dominance effect on each chromosome (since all QTL must have an additve effect, this value must be equal or smaller than num.add.qtl.chr).

pos.add.qtl:

Object of class "list". This list holds information on the positions of the QTL with additive effects (hence all). There should be two elements in this list: ID, an integer vector giving the IDs of the QTL; M, a numeric vector giving their map positions.

pos.dom.qtl:

Object of class "list". Same as for pos.add.qtl, but only for QTL with dominance effects. Because only QTL with additive effects can have dominance effects, the elements must be subsets of the corresponding elements if pos.add.qtl.

add.and.dom.eff:

Object of class "list". There should be two elements in this list: add, a numeric vector with the additve effects; dom, a numeric vector with the dominance effects.

num.per.mar.chr:

Object of class "integer". An integer value giving the number of perfect markers on each chromosome. A perfect marker is a QTL that is observed as a SNP.

per.mar.id:

Object of class "integer". An integer vector giving the IDs of the perfect markers.

Methods

hypredCode

signature(object = "hypredGenome"): Create design matrices of SNP effects for a set of individuals.

hypredFounder

signature(object = "hypredGenome"): Create the gametes of two homozygous founder lines that differ at each locus.

hypredNewMap

signature(object = "hypredGenome"): Modify the genetic map of the object

hypredNewQTL

signature(object = "hypredGenome"): Assign QTLs to the object.

hypredRecombine

signature(object = "hypredGenome"): Recombine two haploid genomes.

hypredSNPdist

signature(object = "hypredGenome"): Determine the distance and recombination frequency between two loci on a chromosome.

hypredTruePerformance

signature(object = "hypredGenome"): Determine the genotypic performance of individuals

hypredTpGenomeSpecific

signature(object = "hypredGenome"): Determine the genome specific genotypic performance of individuals

show

signature(object = "hypredGenome"): Print some summary information about the genome

summary

signature(object = "hypredGenome"): Print some summary information about the genome.

Warning

To assure a valid object, this object should only be created by the function hypredGenome, and modified with the functions hypredNewMap and hypredNewQTL.

Note

The number of SNP, QTL with additive effect, QTL with dominance effect, and perfect markers must be the same for each chromosome. This restriction helps allot in keeping track of the loci.

The ID of a loci is its running number, where the first locus (the one with lowest map position) on chromosome 1 has ID = 1, the second locus (the one with the second lowest map position) on chromosome 1 has ID = 2 and so on. When there are 10 loci per chromosome, then ID = 11 belongs to the first locus on chromosome 2.

Author(s)

Frank Technow

See Also

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.

Examples

showClass("hypredGenome")

timflutre/hypred documentation built on May 6, 2019, 10:51 a.m.