sim.mcmc: Simulations to test QTL analyses

In kbroman/qtlsim: Software for Testing QTL Analysis via Simulations

Simulations to test QTL analyses

Description

Run multiple simulations of a backcross, analyzed using several model selection techniques, including MCMC.

Usage

sim.mcmc(n.sim=1000, max.steps=28, bic.mult=2.5, n.steps=1000,
         n.ind=100, n.mar=rep(11,9), mar.sp=rep(10,10*9),
         qtl.chr=c(1,1,2,2,3,4,5), qtl.mar=c(4,8,4,8,6,4,1),
         qtl.dist=rep(0,7), qtl.eff=c(1,1,1,-1,1,1,1)/2,
         sigma=1, only.two=FALSE)

Arguments

n.sim	Number of simulation replicates.
max.steps	Maximum number of steps in forward/backward selection.
bic.mult	Multiplier for BIC.
n.steps	Number of steps in MCMC.
n.ind	Number of backcross individuals.
n.mar	Vector indicating the number of markers on each chromosome.
mar.sp	Vector of length sum(n.mar)-n.chr-1, giving the inter-marker spacings in cM.
qtl.chr	Chromosomes on which qtls are sitting.
qtl.mar	Markers to the left of each qtl, numbered 1, 2, ...
qtl.dist	Distance between qtl and marker to left, in cM.
qtl.eff	QTL effects.
sigma	Residual (environmental) standard deviation.
only.two	If TRUE, only do forward selection and MCMC

Value

A list of three components. The first is a list of length 5, whose components correspond to the results of forward and backward selection, the same followed by branch-and-bound, with BIC, and MCMC. (Each component of this list is itself a list of length n.sim, with each component giving the chromosome numbers and marker numbers of the identified QTLs.) The second component of the main list gives the BIC values corresponding to the identified models. The last component gives the step at which the final model from MCMC was first observed, plus the number of distinct models observed.

Author(s)

Karl W Broman, [e-mail]

References

Broman, K. W. (1997) Identifying quantitative trait loci in experimental crosses. PhD dissertation, Department of Statistics, University of California, Berkeley.

See Also

simbc, anal.mcmc, anal.leaps, anal.multi

Examples

## Not run: results <- sim.mcmc(n.sim=10)

kbroman/qtlsim documentation built on May 17, 2023, 11:53 p.m.