qtlbim: QTL Bayesian Interval Mapping

library(qtlbim)

## Simulate small backcross.
cross <- qb.sim.cross(len = rep(60,3), n.mar = 7, eq.spacing =FALSE,
  n.ind = 100, type = "bc", ordinal = c(0.3,0.3,0.2,0.2),
  missing.geno = 0.03, missing.pheno = 0.03,
  qtl.pos = rbind(qtl.1=c(chr=1,pos=15), qtl.2=c(1,45),
                  qtl.3=c(2,12), qtl.4=c(3,15)),
  qtl.main = rbind(main.1=c(qtl=1,add=1.5), main.2=c(2,0),
                   main3=c(3,-1), main4=c(4,0)),
  qtl.epis = rbind(epis1=c(qtl.a=2,qtl.b=3,aa=-2), epis2=c(2,4,3)),
  covariate = c(fix.cov=0.5,ran.cov=0.07),
  gbye = rbind(GxE.1=c(qtl=3,add=2)))

## Summary of simulation information.
summary(cross$qtl)

## Compute genotype probabilities and run MCMC.
cross <- qb.genoprob(cross, step=2) 

## Create MCMC samples
## First line as qb.data options; second line has qb.model options.
qbExample <- qb.mcmc(cross, pheno.col = 3, rancov = 2, fixcov = 1,
  chr.nqtl = rep(3,nchr(cross)), intcov = 1, interval = rep(10,3),
  n.iter = 1000, n.thin = 20)