NAMESPACE

# Generated by roxygen2: do not edit by hand

export(JaBbA)
export(Rcplex2)
export(read.junctions)
import(DNAcopy)
import(GenomicRanges)
import(Matrix)
import(data.table)
import(gGnome)
import(gTrack)
import(gUtils)
import(igraph)
import(optparse)
import(parallel)
importFrom(DNAcopy,CNA)
importFrom(DNAcopy,segment)
importFrom(DNAcopy,smooth.CNA)
importFrom(GenomeInfoDb,seqlengths)
importFrom(Ppurple,ppurple)
importFrom(VariantAnnotation,geno)
importFrom(VariantAnnotation,info)
importFrom(VariantAnnotation,readVcf)
importFrom(gplots,col2hex)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,hist)
importFrom(graphics,plot)
importFrom(graphics,title)
importFrom(methods,as)
importFrom(methods,is)
importFrom(rtracklayer,import)
importFrom(sequenza,baf.model.fit)
importFrom(sequenza,get.ci)
importFrom(sequenza,segment.breaks)
importFrom(stats,C)
importFrom(stats,aggregate)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,ppois)
importFrom(stats,predict)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(utils,read.delim)
importFrom(utils,write.table)
useDynLib(JaBbA)