NAMESPACE

# Generated by roxygen2: do not edit by hand

export(alleleCount)
export(ascatNgsToBattenberg)
export(ascatToBattenberg)
export(collate_bb_subclones)
export(concat_files)
export(createPng)
export(createProjectFile)
export(dpIn2vcf)
export(dumpCounts.Broad)
export(dumpCounts.DKFZ)
export(dumpCounts.ICGCconsensusIndel)
export(dumpCounts.ICGCconsensusSNV)
export(dumpCounts.Muse)
export(dumpCounts.Sanger)
export(dumpCounts.StrelkaIndel)
export(dumpCounts.cgpPindel)
export(dumpCounts.mutect)
export(dumpCounts.scalpel)
export(filterForDeaminase)
export(filterForSignature)
export(getAltAllele)
export(getTrinucleotideContext)
export(identifyKataegis)
export(mut_cn_phasing)
export(mut_mut_phasing)
export(mutationBurdenToMutationCopyNumber)
export(mutationCopyNumberToMutationBurden)
export(parseFai)
export(parseIgnore)
export(plot_ccf_hist)
export(plot_mcn_hist)
export(plot_vaf_hist)
export(runGetDirichletProcessInfo)
export(split_by_chrom)
export(vcf2loci)
import(GenomicRanges)
import(VariantAnnotation)
import(ggplot2)
importFrom(IRanges,IRanges)
importFrom(Rsamtools,scanFa)
importFrom(S4Vectors,DataFrame)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(methods,as)
importFrom(reshape2,melt)
importFrom(stats,mad)
importFrom(stats,na.omit)
importFrom(stats,prop.test)
importFrom(stats,quantile)
importFrom(stats,runmed)
importFrom(stats,sd)
importFrom(utils,head)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)