#exportPattern("^[[:alpha:]]+")
export(
addCNV, 
addCoverage, 
addSeqPref, 
addPatternDensity, 
addOffset,
addLibraryFactors,
addEnrichmentParameters, 
makeTable, 
isSignificant,
getPCA,
plotCNV,
plotCoverage, 
plotEnrichmentProfile,
plotEPmatrix,
regionStats, 
createQseaSet,
normMethod, 
addContrast, 
fitNBglm,
getExampleQseaSet,
addNewSamples
)

exportMethods(
getSampleTable,
getSampleNames,
getSampleGroups,
getChrNames,
getParameters,
#addParameters,
getRegions,
getWindowSize,
getLibSize,
getOffset,
getCNV,
hasCNV,
getCounts,
getZygosity, 
setZygosity,
plotPCA,
plotPCAfactors
)

exportClasses(
    "qseaSet", 
    "qseaGLM", 
    "qseaPCA" 
)

importClassesFrom(methods, character, numeric)
importMethodsFrom(methods, show)
importMethodsFrom(BiocGenerics, plotPCA)
importMethodsFrom(Biostrings, matchPattern, reverseComplement, vcountPattern)
importMethodsFrom(BSgenome, getSeq)
importMethodsFrom(IRanges, cor, start,end, quantile, ranges, "ranges<-", 
    resize, restrict, values, var, width,unique,as.vector, which, overlapsAny, 
    as.matrix, as.data.frame, '[', Views, viewSums, nir_list, collapse)
importMethodsFrom(methods, show)
importMethodsFrom(GenomicRanges, as.data.frame, length, '[',
    reduce, coverage, findOverlaps, countOverlaps, disjointBins)
importFrom(zoo, rollapply)
importFrom(HMMcopy, HMMsegment)
importFrom(rtracklayer,import )
importFrom(limma, contrastAsCoef)
importFrom(GenomicRanges, GRanges, seqnames, 
    as.data.frame, mcols, "mcols<-", 
    reduce, coverage, findOverlaps, countOverlaps, disjointBins)
importFrom(Biostrings, DNAString, DNAStringSet, maskMotif, masks)
importFrom(BSgenome, bsapply,getBSgenome)
importFrom(graphics, abline, legend, lines, plot)
importFrom(gtools, mixedsort)
importFrom("utils", "head")
importFrom("methods", "new")
importFrom(BiocParallel,bplapply,bpmapply,SerialParam,bpparam,bpworkers,
    bpstart,bpstop )
importFrom(IRanges, cor, end, quantile, ranges, "ranges<-", resize, 
    restrict, start, values, var, width,unique, which, IRanges,space,
    as.matrix, as.data.frame, Views, viewSums, nir_list, collapse)
importFrom(stats, lm, t.test, wilcox.test, qnbinom)
importFrom(utils, read.table, setTxtProgressBar, txtProgressBar,write.table)
importFrom(Rsamtools, scanBam,ScanBamParam,scanBamFlag)
importFrom(GenomeInfoDb, seqinfo, seqnames, seqlevels, seqlengths, Seqinfo,"seqlevels<-" )
importFrom(grDevices, colorRamp, colorRampPalette, dev.off, png, rgb)
importFrom(graphics,abline, legend, lines, plot, arrows, axis, box, frame, 
    image, layout, par, points, rect, smoothScatter, symbols, text)
importFrom(stats, as.dendrogram, as.dist, dist, hclust, median, na.omit, optim, 
    p.adjust, pchisq, pgamma,qgamma, pnorm, qpois, rnbinom, sd)
useDynLib(qsea, Cdqrls)

