run.bmapqtl      run Bmapqtl.exe from inside R
bmapqtl.options  options for Bayesian interval mapping MCMC sampling

plot.bim	 create all bim diagnostic plots
plot.bim.diag    marginal and conditional graphical summaries of diagnostics
plot.bim.effects histogram of QTL loci plus scatterplots of effects
plot.bim.fdr     plot curves for QTL false discovery rate
plot.bim.loci    jittered chromosome plot of QTL loci
plot.bim.mcmc    plot of burnin and mcmc sequence diagnostics
plot.bim.model   model selection: runs bim.nqtl and bim.pattern
plot.bim.qtl     density of QTL loci suitable for overlay plots

summary.bim      summary of bim object from read.bim
summary.bim.model summary of object from bim.model 
summary.bim.qtl  summary of object from bim.qtl or bim.effects

Bnapus           cross object for Brassica napus full data
fisch            cross object for fisch simulated data
fisch.bim        bim object for fisch simulated data
vern             cross object for Brassica napus 8-week vernalization data
verngeo.bim      Bayesian interval map samples of vern using geometric 3 prior
vernpois.bim     Bayesian interval map samples of vern using Poisson 3 prior

subset.bim       subsetting of bim object

bim.fdr          estimate false discovery rate features
bim.model        estimate posterior and Bayes factors for number and pattern of QTL
bim.nqtl         estimate posterior and Bayes factors for number of QTL
bim.pattern      estimate posterior and Bayes factors for chromosome pattern of QTL
bim.qtl          density and point estimates for QTL loci

read.bim         read Bayesian interval mapping samples from WinQTL output
read.bmapqtl     read nval.dat file used by WinQTL
write.bmapqtl    write nval.dat file used by WinQTL

