# Generated by roxygen2: do not edit by hand

export(attachContext)
export(attachMutType)
export(countMutTypes)
export(decipherMutationalProcesses)
export(extractXvarlinkData)
export(filterSNV)
export(frequencize)
export(getCosmicSignatures)
export(importVCFfiles)
export(matchSignatures)
export(plotMutTypeProfile)
export(plotSignExposures)
export(prelimProcessAssess)
export(processVCFdata)
export(removeMismatchMut)
export(resolveMutSignatures)
export(revCompl)
export(setMutClusterParams)
export(silhouetteMLB)
export(simplifySignatures)
export(sortByMutations)
export(table2df)
exportClasses(mutFrameworkParams)
exportClasses(mutSignExposures)
exportClasses(mutationCounts)
exportClasses(mutationSignatures)
exportMethods("[")
exportMethods(as.data.frame)
exportMethods(as.list)
exportMethods(as.matrix)
exportMethods(as.mutation.counts)
exportMethods(as.mutation.signatures)
exportMethods(as.mutsign.exposures)
exportMethods(cbind2)
exportMethods(coerceObj)
exportMethods(getCounts)
exportMethods(getFwkParam)
exportMethods(getMutationTypes)
exportMethods(getSampleIdentifiers)
exportMethods(getSignatureIdentifiers)
exportMethods(msigPlot)
exportMethods(setFwkParam)
import(foreach)
importFrom(cluster,silhouette)
importFrom(doParallel,registerDoParallel)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,box)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,title)
importFrom(methods,callNextMethod)
importFrom(methods,cbind2)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,slotNames)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(pracma,squareform)
importFrom(proxy,dist)
importFrom(stats,median)
importFrom(stats,quantile)
importFrom(stats,rmultinom)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
