useDynLib(CNVassoc)

import(
CNVassocData, 
mixdist, 
mclust, 
survival
)

export(
cnv,
is.cnv,
CNVassoc,
CNVtest,
getProbs,
getProbsRegions,
getPvalBH,
getQualityScore,
mixture,
multiCNVassoc,
simCNVdataBinary,
simCNVdataNorm,
simCNVdataCaseCon,
simCNVdataPois,
simCNVdataWeibull,
plotSignal,
fastCNVassoc,
fastCNVinter
)

importFrom("graphics", "abline", "axis", "barplot", "layout", "legend", "lines", "locator", "par", "plot", "points", "polygon")

importFrom("stats", "as.formula", "coef", "contrasts", "cor", "dbinom", "density", "dnorm", "dpois", "dweibull", "glm", "glm.control", "integrate", "logLik", "model.matrix", "model.response", "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "printCoefmat", "pweibull", "qnorm", "rbinom", "rmultinom", "rnorm", "rpois", "rweibull", "sd")


S3method(print, cnv)
S3method(plot, cnv)

S3method(anova, CNVassoc)
S3method(logLik, CNVassoc)
S3method(print, CNVassoc)
S3method(summary, CNVassoc)
S3method(print, anova.CNVassoc)
S3method(print, summary.CNVassoc)

S3method(print, QualityScore)
S3method(getQualityScore, cnv)
S3method(getQualityScore, default)

S3method(print, CNVtest)

S3method(getProbs, cghCall)
S3method(getProbs, cnv)

S3method(subset, cnv)

# not exported:
  # assocCNV.i
  # classCNV
  # EMlogistic
  # EMnorm
  # getQualityScoreDefault
  # hessianLinear
  # hessianLogistic
  # linear.fit
  # logistic.fit
  # logLike.logistic
  # logLike.norm
  # matrix2vector
  # mix
  # NRlogistic
  # NRnorm
  # plot.cnv.intensities
  # plot.cnv.norm
  # vector2matrix
  # is.quantitative
  # getProbsRegions.i
  # Others ...

