MMAPPR2/NAMESPACE at main · jonathonthill/MMAPPR2 · GitHub

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# Generated by roxygen2: do not edit by hand

export(calculateDistance)
export(generateCandidates)
export(loessFit)
export(mmappr)
export(mmapprData)
export(mmapprParam)
export(outputMmapprData)
export(peakRefinement)
export(prePeak)
export(tempOutputFolder)
exportMethods("distancePower<-")
exportMethods("fileAggregation<-")
exportMethods("gtf<-")
exportMethods("homozygoteCutoff<-")
exportMethods("includeScaffolds<-")
exportMethods("loessOptCutFactor<-")
exportMethods("loessOptResolution<-")
exportMethods("minBaseQuality<-")
exportMethods("minDepth<-")
exportMethods("minMapQuality<-")
exportMethods("mutFiles<-")
exportMethods("outputFolder<-")
exportMethods("param<-")
exportMethods("peakIntervalWidth<-")
exportMethods("refFasta<-")
exportMethods("wtFiles<-")
exportMethods(candidates)
exportMethods(distancePower)
exportMethods(fileAggregation)
exportMethods(gtf)
exportMethods(homozygoteCutoff)
exportMethods(includeScaffolds)
exportMethods(loessOptCutFactor)
exportMethods(loessOptResolution)
exportMethods(minBaseQuality)
exportMethods(minDepth)
exportMethods(minMapQuality)
exportMethods(mutFiles)
exportMethods(outputFolder)
exportMethods(param)
exportMethods(peakIntervalWidth)
exportMethods(peaks)
exportMethods(refFasta)
exportMethods(snpDistance)
exportMethods(wtFiles)
import(BiocParallel)
import(GenomeInfoDb)
import(GenomicRanges, except = c(shift))
import(Rsamtools)
import(data.table)
importFrom(Biostrings,DNAStringSet)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(IRanges,subsetByOverlaps)
importFrom(SummarizedExperiment,assays)
importFrom(VariantAnnotation,alt)
importFrom(VariantAnnotation,altDepth)
importFrom(VariantAnnotation,predictCoding)
importFrom(VariantAnnotation,totalDepth)
importFrom(VariantTools,TallyVariantsParam)
importFrom(VariantTools,callVariants)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,graphics.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,polygon)
importFrom(stats,approxfun)
importFrom(stats,density.default)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,var)
importFrom(utils,capture.output)
importFrom(utils,object.size)
importFrom(utils,sessionInfo)
importFrom(utils,str)
importFrom(utils,tail)
importFrom(utils,write.table)
importFrom(VariantTools,pileupVariants)
importFrom(Rsamtools,ApplyPileupsParam)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,indexFa)