hypredGenome: Define genome parameters

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

Description

This function is used to define the genome parameters: number and length of chromosomes, number of SNP markers and haplotype blocks. This function also performes part of the simulation, by simulating a genetic map (which can be modified later).

Usage

 hypredGenome(num.chr, len.chr, num.snp.chr, num.blocks.chr = NULL) 

Arguments

num.chr	Integer argument indicating the number of chromosomes.
len.chr	Numeric vector giving the length of each chromosome in Morgan. This vector must have as many elements as there are chromosomes.
num.snp.chr	Integer value indicating the number of SNP markers per chromosome.
num.blocks.chr	Integer value indicating the number of haplotype blocks per chromosome. Default is NULL.

Details

loci

The markers are interpreted and treated as SNP with two alleles, 1 and 0. The number of SNP marker is the same for each chromosome.

map positions

The map positions of all loci are sampled from the uniform distribution over the interval (0,L), where L is the length of the chromosome in Morgan.

haplotype blocks

All SNP that are located on one block are treated as perfectly linked. All functions that use the map positions have arguments to indicate wheter the block positions of QTL and SNP should be used or their individual positions.

If the argument is non NULL, then the following condition must hold,
(num.blocks.chr/num.snp.chr) < 0.1001, else there is an error.

The number of loci on all blocks but the last is:
floor(num.snp.chr/num.block.chr)
If num.snp.chr mod num.block.chr != 0, the last block will contain more loci than the other blocks.

The map position of a block is the one of its center SNP. These center SNP are found as follows:

block1: floor(num.snp.chr/ (2*num.block.chr))

block2: floor(num.snp.chr/ (2*num.block.chr)) +
1* floor(num.snp.chr/num.block.chr)

block3: floor(num.snp.chr/ (2*num.block.chr)) +
2 * floor(num.snp.chr/num.block.chr)

and so on.

Value

An object of class "hypredGenome"

Note

Some of the results of this function are subject to randomness. To obtain reproducible results, you should use set.seed() to set a seed for the random number generator.

Author(s)

Frank Technow

See Also

The function hypredNewMap which allows to modify the genetic map. The function hypredNewQTL which allows to assign QTL or modify already existing ones.

Examples

gen.def <- hypredGenome(num.chr = 2, 
                        len.chr = c(1.0,1.2),
                        num.snp.chr = 90)


summary(gen.def)

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