# Generated by roxygen2: do not edit by hand
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# IMPORTS
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importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, MIAxE,
    Versioned, VersionedBiobase, Versions)
importClassesFrom(QDNAseq, QDNAseqCopyNumbers, QDNAseqReadCounts)
importClassesFrom(GenomicRanges, GRanges)

importMethodsFrom(Biobase, AnnotatedDataFrame, assayData, classVersion, fData,
    "fData<-", featureData, featureNames, pData, "pData<-", phenoData,
    sampleNames, "sampleNames<-", varMetadata)

importFrom(Biobase, assayDataElement, "assayDataElement<-",
    assayDataElementNames, assayDataElementReplace, assayDataNew, sampleNames)
importFrom(stats, sd, cor, t.test, wilcox.test, median, mad, pnorm, rnorm, p.adjust, na.exclude, binom.test)
importFrom(utils, data, maintainer, packageVersion, read.table, write.table, tail)
importFrom(grDevices, dev.off, pdf, png)
importFrom(methods, is)

import(ggplot2)


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# EXPORTS
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#exportPattern("^[[:alpha:]]+")

export("runACE")
export("ploidyplotloop")
export("singlemodel")
export("squaremodel")
export("singleplot")
export("analyzegenomiclocations")
export("getadjustedsegments")
export("objectsampletotemplate")
export("linkvariants")
export("postanalysisloop")
export("twosamplecompare")
export("ACEcall")
export("squaremodelsummary")
export("loopsquaremodel")
export("templatefromequalsegments")
export("segmentstotemplate")
export("compresstemplate")
export("correlationmatrix")
export("correlationmatrixadjusted")
export("forcesegmentsontemplate")


# EOF
