run.bmapqtl {bim}R Documentation

Run Bmapqtl reversible jump MCMC

Description

Run Bmapqtl reversible jump MCMC

Usage

run.bmapqtl(cross, pheno=1, chrom=0, result.file="")

Arguments

cross An object of class "cross"
pheno phenotypic trait number or name
chrom chromosome number (0 = all). Note that at this stage, it can either be all chromosomes (0) or a single chromosome.
result.file Result file name. If this is specified, the result will be written to a tab-delimited text file. If it is an empty string (""), result will not be output as a file.

Value

The result is an object of class "bim", which is a list with the following components:

bmapqtl parameter settings for Bmapqtl run
burnin burnin sequence data frame, containing niter = iteration number, nqtl = number of QTL, LOD = LOD score based on simulated QTL genotypes, mean = grand mean of phenotype, envvar = environmental variance, addvar = additive variance, domvar = dominance variance (if included), and herit = heritability.
iter MCMC iteration summary data frame, with same elements as burnin.
loci data frame with MCMC estimates across loci by iteration, containing niter = iteration number, nqtl = number of QTL, chrom = chromosome number, locus = locus position in centi-Morgans, add = additive effect, dom = dominance effect (if included).

Author(s)

Hao Wu, hao@jax.org

References

  • http://www.stat.wisc.edu/~yandell/qtl/data/osborn/Bnapus
  • JM Satagopan, BS Yandell, MA Newton and TC Osborn (1996) Markov chain Monte Carlo approach to detect polygene loci for complex traits. Genetics 144: 805-816. http://www.genetics.org/cgi/content/abstract/144/2/805 [first MCMC for experimental crosses; analysis of B. napus N2=LG9 (see vern data)]
  • JM Satagopan and BS Yandell (1996) Estimating the number of quantitative trait loci via Bayesian model determination. Special Contributed Paper Session on Genetic Analysis of Quantitative Traits and Complex Diseases, Biometrics Section, Joint Statistical Meetings, Chicago, IL. ftp://ftp.stat.wisc.edu/pub/yandell/revjump.html [first RJ-MCMC for experimental crosses; analysis of B. napus N2=LG9; see vern data]
  • Gaffney PJ (2001) An efficient reversible jump Markov chain Monte Carlo approach to detect multiple loci and their effects in inbred crosses. PhD Dissertation, Dept of Statist, UW-Madison. http://wwwlib.umi.com/dissertations/fullcit/301245

    See Also

    plot.bim, read.bim

    Examples

    data(vern)
    ## Not run: 
    bim = run.bmapqtl(vern)
    plot(bim)
    ## End(Not run)
    

    [Package bim version 1.01-1 Index]