#  All functions exported other than those starting with "."
exportPattern("^[^\\.]")

import(methods)
importFrom("stats", "binomial", "coef", "contrasts<-", "contr.sum", "dbeta", "dbinom", "dlogis",
           "glm", "lm.fit", ".lm.fit", "lm.wfit", "model.matrix", "optim", "optimize",
           "pbeta", "pbinom", "plogis", "qlogis", "quantile", "rbinom", "rnorm", "sd", "var")
importFrom("graphics", "arrows", "axis", "legend", "lines")
importFrom("data.table", "fread")
importFrom("statmod", "gauss.quad.prob", "logmdigamma")
importFrom("limma", "plotMDS", "squeezeVar")

# Extra imports for voomaLmFitWithImputation
importFrom("stats", "approxfun", "hat", "lowess", "median", "runif")
importFrom("graphics", "title")
importFrom("limma", "arrayWeights", "asMatrixWeights", "chooseLowessSpan", "duplicateCorrelation",
           "loessFit", "lmFit")

importClassesFrom("limma", "EList", "EListRaw", "MDS")

S3method(dpcImpute,default)
S3method(dpcImpute,EList)
S3method(dpcQuant,default)
S3method(dpcQuant,EList)
S3method(filterCompoundProteins,default)
S3method(filterCompoundProteins,EList)
S3method(filterCompoundProteins,EListRaw)
S3method(filterNonProteotypicPeptides,default)
S3method(filterNonProteotypicPeptides,EList)
S3method(filterNonProteotypicPeptides,EListRaw)
S3method(filterSingletonPeptides,default)
S3method(filterSingletonPeptides,EList)
S3method(filterSingletonPeptides,EListRaw)
S3method(imputeByExpTilt,default)
S3method(imputeByExpTilt,EList)
S3method(imputeByExpTilt,EListRaw)
S3method(plotPeptides,default)
S3method(plotPeptides,EList)
S3method(removeNARows,default)
S3method(removeNARows,EList)
