## Imports:
importFrom(bnlearn, nodes, hc, averaged.network, bn.boot, custom.strength,
           arcs, "arcs<-", empty.graph, score, pdag2dag, discretize,
           tiers2blacklist, bn.fit,  boot.strength, random.graph,
           graphviz.plot, children, parents)

## BiocCheck did not pass without including 'graph' in the dependencies due to
## a problem in bnlearn package.
importFrom(graph, plot)
importFrom(parallel, makeCluster, stopCluster)  ## BiocParallel is better
importFrom(pheatmap, pheatmap)
importFrom(matrixStats, colSds, rowSds)
importFrom(C50, C5.0, C5.0Control, as.party.C5.0)
importFrom(MASS, rlm)
importFrom(partykit, as.party)
importFrom(Rgraphviz, getDefaultAttrs)

## Imported by WGCNA but not installed with it:
import(GO.db)
importFrom(impute, impute.knn)
importFrom(preprocessCore, normalize.quantiles)
importFrom(stats, as.formula, oneway.test, setNames)

## Recommended by Bioconductor:
importFrom(grDevices, dev.new, dev.off, png, rgb)
importFrom(graphics, abline, arrows, barplot, hist, legend,
           par, plot.new, points)
importFrom(utils, assignInNamespace, capture.output, read.csv,
           tail, write.csv)
importFrom(stats, manova, p.adjust, predict, quantile,
           rnorm, runif, sd, summary.aov, t.test, var) ## cor was not imported because:
## cor must be imported from WGCA otherwise stats::cor will be used by WGCNA functions leading to errors.
importFrom(WGCNA, blockwiseModules, moduleEigengenes, allowWGCNAThreads, pickSoftThreshold, labels2colors, sizeGrWindow, plotDendroAndColors, cor)
## IMPORTANT: In this package, use "stats::cor" instead of "cor" otherwise the "WGCNA::cor" is used by default.

## Exports:
##exportPattern("^[[:alpha:]]+")
exportClasses(pigengene)
export(one.step.pigengene, check.pigengene.input, balance, calculate.beta,
       wgcna.one.step, compute.pigengene, plot.pigengene, pheatmap.type,
       project.eigen, learn.bn, draw.bn, make.decision.tree, get.used.features,
       get.fitted.leaf, module.heatmap, compact.tree, get.genes, preds.at,
       pvalues.manova, gene.mapping, dcor.matrix, check.nas)
S3method(plot, pigengene)
