run.bmapqtl {bim} | R Documentation |
Run Bmapqtl reversible jump MCMC
run.bmapqtl(cross, pheno=1, chrom=0, result.file="")
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. |
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). |
Hao Wu, hao@jax.org
vern
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vern
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data(vern) ## Not run: bim = run.bmapqtl(vern) plot(bim) ## End(Not run)