exportPattern("^[[:alpha:]]+")
import(methods)
import(limma)
import(Gviz)
import(GenomicRanges)
import(Seqinfo)
import(bsseq)
import(IRanges)
import(SummarizedExperiment)
import(ExperimentHub)
import(AnnotationHub)
importFrom("plyr", rbind.fill)
importFrom("graphics", plot)
importFrom("S4Vectors", subjectHits, queryHits)
importFrom("stats", approx, p.adjust, pchisq, pnorm, qnorm)
importFrom("edgeR", modelMatrixMeth)
importFrom("utils", data)
importFrom("minfi", detectionP, preprocessFunnorm, getM, makeGenomicRatioSetFromMatrix, getBeta, getAnnotation, ilogit2, logit2)
importFrom("missMethyl", goregion, varFit, contrasts.varFit, topVar)
importFrom("biomaRt", useEnsembl, useMart)
importFrom("Gviz", BiomartGeneRegionTrack)
importFrom("grDevices", colorRampPalette)
export(dmrcate)
exportMethods(cpg.annotate, sequencing.annotate, rmSNPandCH, DMR.plot, extractRanges, changeFDR, getCollapsedBetas)
