qbExample: MCMC sample for fake BC example

In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description

Retrieve or recreate MCMC samples used in qtlbim.pdf document and demos.

Usage

data(qbExample)

Details

This example is used in vignettes and demos. See vignette qtlbim.pdf or see qtlbim.Rnw in doc folder of package.

See Also

qb.genoprob, qb.mcmc, qb.sim.cross

Examples

data(qbExample)
summary(qbExample)

## Not run: 
## Fake BC Example.
set.seed(1234)
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(cross$qtl)
cross <- qb.genoprob(cross, step=2)
qbExample <- qb.mcmc(cross, pheno.col = 3, rancov = 2, fixcov = 1,
                     chr.nqtl = rep(3,nchr(cross)), intcov = 1, seed = 1216,
                     interval = rep(10,3), n.iter = 1000, n.thin = 20)

save("qbExample", file = "qbExample.RData")

## End(Not run)

fboehm/qtlbim documentation built on Feb. 16, 2021, 12:04 a.m.