useDynLib(podkat)

import(Rcpp)
import(methods)
importFrom(stats, qqplot, p.adjust, p.adjust.methods, dbeta,
           glm, lm, median, model.frame, model.matrix, model.response,
           na.omit, pchisq, ppoints, rbinom, residuals, rnorm, var)
importFrom(graphics, plot, abline, axTicks, axis, box, mtext,
           par, points, segments, text)
importFrom(grDevices, col2rgb, rainbow, rgb)
importFrom(utils, read.table)
importFrom(parallel, makePSOCKcluster, stopCluster)
importFrom(BiocGenerics, unlist, clusterApplyLB, clusterEvalQ,
           clusterExport, weights, clusterCall)
import(Biobase)
import(Rsamtools)
import(Matrix)
import(GenomeInfoDb)
importFrom(IRanges, IRanges, active, "active<-", "%over%")
import(GenomicRanges)
import(Biostrings)
importFrom(BSgenome, BSgenome, MaskedBSgenome)

export(computeKernel, unmaskedRegions, readSampleNamesFromVcfHeader,
       readRegionsFromBedFile, betaWeights, logisticWeights, invSdWeights)
exportClasses(NullModel, AssocTestResult, AssocTestResultRanges,
              VariantInfo, GenotypeMatrix)
exportMethods(show, summary, print, nullModel, assocTest, p.adjust,
              variantInfo, MAF,
              genotypeMatrix, readGenotypeMatrix, readVariantInfo,
              partitionRegions, filterResult, qqplot, plot, sort, c,
              "[", residuals, coefficients, split, weights, names)

