qbSim: MCMC samples used in scan.pdf document

In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description

Retrieve or recreate MCMC samples used in scan.pdf document.

Usage

data(qbSimMain)
data(qbSimEpi)

Details

Both calls to data create qb objects names qbSim. See vignette scan.pdf or see scan.Rnw in doc folder of package.

See Also

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

Examples

data(qbSimMain)
summary(qbSim)

data(qbSimEpi)
summary(qbSim)

## Not run: 
## Setup for Simulated Data used in scan.pdf.
n.ind <- 100		## number of individuals
n.mark <- 200		## number of markers
by.mark <- 1		## cM spacing between markers
qtl.positions <- n.mark / 2	## position of QTL
markers <- seq(0, n.mark, by = by.mark)
names(markers) <- paste("M", markers, sep = "")
sim.map <- list(ch1 = markers)
sim.model <- matrix(c(1, qtl.positions, qtl.effect / 2), 1, 3)
colnames(sim.model) <- c("chromosome","qtl-position","effect-size")
n.iter <- 1000		## number of iterations for MCMC
qb.random.seed <- 1626  ## random seed for MCMC

## Genetic architecture for scan simulations: 3 QTL.
qtl.positions <- rbind(qtl1 = c(chromosome = 1, locus = 5), 
                       qtl2 = c(chromosome = 1, locus = 50), 
                       qtl3 = c(chromosome = 2, locus = 33) )

qtl.positions
qtl.main.model <-
  rbind(qtl1.main.effect = c(qtl = 1, main.effect.size = 0),
        qtl2.main.effect = c(qtl = 2, main.effect.size = 0),
        qtl3.main.effect = c(qtl = 3, main.effect.size = 0))

qtl.main.model
qtl.epi.model <- rbind(qtl1.and.qtl3.epi.effect =
  c(qtl1 = 1, qtl2 = 3, epi.effect.size = 10))
qtl.epi.model

## SimEpi
set.seed(1234)
sim <- qb.sim.cross(len = rep(100, 2), n.mar = 10, eq.spacing = TRUE, 
                    n.ind = 100, type = "bc", missing.geno = 0.03,
                    qtl.pos = qtl.positions, 
                    qtl.main = qtl.main.model,
                    qtl.epis = qtl.epi.model)
sim <- qb.genoprob(sim)
qbSim <- qb.mcmc(sim, n.iter = n.iter, verbose = FALSE, n.thin = 40,
                 seed = qb.random.seed)

## The next line saves qbSim as an external binary file.
save("qbSim", file = "qbSimEpi.RData")

## SimMain
qtl.main.model[2, "main.effect.size"] = 10
set.seed(1234)
sim <- qb.sim.cross(len = rep(100, 2), n.mar = 10, eq.spacing = TRUE, 
                    n.ind = 100, type = "bc", missing.geno = 0.03,
                    qtl.pos = qtl.positions, 
                    qtl.main = qtl.main.model,
                    qtl.epis = NULL)

## After the data is simulated call qb.genoprob to fill in 
## missing data.
sim <- qb.genoprob(sim, step = 2)

## Call qb.mcmc and then analysis code.
qbSim <- qb.mcmc(sim, n.iter = n.iter, verbose = FALSE, n.thin = 40,
                 seed = qb.random.seed)

## The next line saves qbSim as an external binary file.
save("qbSim", file = "qbSimMain.RData")

## End(Not run)

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