############################################################################
# Export directives.  These directives export functions.  S3 methods for
# classes declared in the package should be declared with the "S3method"
# directive.
#
useDynLib(qtlhot, .registration = TRUE)
export(add.phenos)

importFrom(graphics, abline, axis, image, lines, mtext, par, plot, points,
           rug, segments, text, title)
importFrom(stats, anova, approx, as.formula, cov, cov2cor, dnorm, formula,
           lm, median, model.matrix, na.omit, p.adjust, pbinom, pf, pnorm,
           qnorm, quantile, resid, rnorm, sd, window)
importFrom(utils, write.table)
importFrom(qtl, calc.genoprob, find.marker, find.pheno, find.pseudomarker,
           lodint, nchr, nind, nphe, pull.geno, pull.map, scanone,
           sim.cross, sim.map)
importFrom(mnormt, pmnorm)
importFrom(corpcor, is.positive.definite, make.positive.definite)
  
export(highlod)
export(pull.highlod)
S3method(plot, highlod)
S3method(summary, highlod)
S3method(print, highlod)
S3method(max, highlod)
S3method(quantile, highlod)

export(hotsize)
S3method(hotsize, highlod)
S3method(hotsize, scanone)
S3method(plot, hotsize)
S3method(summary, hotsize)
S3method(print, hotsize)
S3method(max, hotsize)

export(big.phase0)
export(qtlhot.phase0)
## export(sliding.bar.plot)

export(sim.null.cross)
export(sim.null.pheno.data)
export(include.hotspots)
export(filter.threshold)

export(hotperm)
S3method(print, hotperm)
S3method(summary, hotperm)
S3method(quantile, hotperm)
S3method(plot, hotperm)
S3method(print, summary.hotperm)

export(ww.perm)
S3method(print, ww.perm)
S3method(summary, ww.perm)

## CMST Routines.

## export(CausalRocCurve)
## export(GetRocMatrix)

export(SimCrossCausal)
export(GetCommonQtls)
export(CMSTtests)
export(CMSTtestsList)

export(GetCandReg)
export(GetCisCandReg)
export(GetCoMappingTraits)
export(FitAllTests)
export(JoinTestOutputs)
export(PrecTpFpMatrix)
export(p.adjust.np)
export(parallel.qtlhot)

## export(mySimulations)
