sim.bc.progeny {BayesQTLBIC}R Documentation

Simulation of back-cross QTL progeny

Description

Simulate a back-cross QTL progeny with given QTL and markers.

Usage

sim.bc.progeny(n,Vp=NULL,map.pos,qtl.pos)

Arguments

n Number of progeny to simulate.
Vp Vector of variances of QTL effects, as a proportion of total variance. Should sum to less than 1.
map.pos Vector of map positions for markers, or a list with elements map.pos ( vector of map positions for markers) and chrom (vector of corresponding chromosome numbers).
qtl.pos Vector of map positions for QTL, or a list with elements qtl.pos (vector of QTL positions) and chrom (vector of corresponding chromosome numbers). In case Vp is missing, qtl.pos should also contain elements h2qs (vector of QTL heritabilities) and qtl.effect.signs (vector of effect signs).

Details

Recombinations are simulated randomly along the genome for each progeny, and used to generate marker and QTL genotypes. Random error with variance 1 - sum(Vp) is added to the QTL effects to give simulated trait values y.

Value

sim.bc.progeny returns a list with elements x (matrix of marker values) and y (vector of trait values).

Author(s)

R.D. Ball rod.ball@AT@scionresearch.com

Examples

set.seed(1234)
ex1.map.pos <- seq(5,105,by=10)
qtldata200 <- sim.bc.progeny(n=200,Vp=c(0.1,0.2,0.3,0.15,0.25)/2,
      map.pos=list(chrom=rep(1:2,rep(length(ex1.map.pos),2)),
      pos=rep(ex1.map.pos,2)),qtl.pos=list(chrom=rep(1:2,c(3,2)),
                                pos=c(40,50,80,30,55)))

[Package BayesQTLBIC version 1.0-0 Index]