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 ### Imports
 

 import(BiocGenerics)

 import(S4Vectors)

 import(Biobase)

 importClassesFrom(IRanges, NumericList)

 importClassesFrom(methods, ANY, character, environment, formula, list, matrix,

                   missing, "NULL", ".NULL")

 importMethodsFrom(methods, initialize, show)

 importFrom(Biostrings, BStringSet, DNAStringSet)

 importFrom(ggbeeswarm, position_beeswarm)

 importFrom(ggiraph, geom_boxplot_interactive, geom_line_interactive,

            geom_point_interactive, GeomInteractiveBoxplot, GeomInteractiveLine,
            GeomInteractivePoint)

 importFrom(ggplot2, aes, aes_, aes_string, autoplot, element_blank,
            element_text, geom_hline, ggplot, guide_legend, guides, layer,
            scale_x_continuous, scale_x_discrete, scale_y_continuous,

            stat_boxplot, theme, theme_get, rel, scale_colour_manual, 
            scale_shape_manual, element_line, unit, margin, 
            element_rect, geom_segment, scale_linetype_manual, 
            geom_text)

 importFrom(grDevices, colorRampPalette)

 importFrom(ggthemes, tableau_color_pal)

 importFrom(IRanges, NumericList)

 importFrom(methods, as, callGeneric, callNextMethod, is, validObject, new)

 importFrom(pheatmap, pheatmap)
 importFrom(RColorBrewer, brewer.pal)

 importFrom(stats, as.formula, coef, lm, model.frame, qnorm, quantile, update,
            reorder)

 importFrom(utils, read.csv, write.csv)

 
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 ### Export S4 classes
 

 exportClasses(SignatureSet, NanoStringRccSet)

 
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 ### Export S4 generics
 

 export("weights<-",
        NanoStringRccSet,

        sData, svarLabels, groups, "groups<-", version, "version<-",

        signatures, "signatures<-", signatureScores, signatureGroups,

        endogenousSubset, housekeepingSubset, getSigFuncs,

        negativeControlSubset, positiveControlSubset,

        controlSubset, nonControlSubset, signatureSubset,

        assayDataApply, signatureScoresApply, esBy,

        munge, signatureFuncs, "setSignatureFuncs<-", "setSignatureGroups<-",

        setQCFlags)

 
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 ### Export S4 methods
 

 exportMethods(show,
               weights, "weights<-", length, names, lengths,

               NanoStringRccSet, groups, "groups<-", version, "version<-",

               sData, svarLabels, dimLabels, "dimLabels<-",

               signatures, "signatures<-", signatureScores,

               design, "design<-", signatureGroups,

               summary, "[", subset, "setSignatureFuncs<-", "setSignatureGroups<-",

               endogenousSubset, housekeepingSubset,
               negativeControlSubset, positiveControlSubset,

               controlSubset, nonControlSubset, signatureSubset,

               assayDataApply, signatureScoresApply, esBy, with,

               munge, transform, getSigFuncs, signatureFuncs,

               setQCFlags, normalize)

 
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 ### Export non-generic functions
 

 export(SignatureSet,
        readNanoStringRccSet,

        readRccFile,
        readRlfFile,

        writeNanoStringRccSet,

        fThresh, fCenter, fScale,
        sThresh, sCenter, sScale,

        fIntThresh, fIntCenter, fIntScale,
        sIntThresh, sIntCenter, sIntScale,

        fAbove, fBelow, fAtLeast, fAtMost,
        sAbove, sBelow, sAtLeast, sAtMost,

        logt, log2t,

        geom_beeswarm_interactive, update_geom_params)

 
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 ### Export S3 methods
 
 S3method(ggplot, NanoStringRccSet)

 S3method(autoplot, NanoStringRccSet)