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NAMESPACE
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148 lines (147 loc) · 4.45 KB
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# Generated by roxygen2: do not edit by hand
export(addReadStats)
export(addSeqContext)
export(annotateReadSegments)
export(calcReadStats)
export(checkSEValidity)
export(countMismatchStatePairs)
export(countStatePairs)
export(estimateNoise)
export(estimateSNR)
export(expandSEToBaseSpace)
export(extractSeqContext)
export(filterPositions)
export(filterReads)
export(filterReadsModBam)
export(flattenReadLevelAssay)
export(getReadLevelAssayNames)
export(getReadLevelColDataNames)
export(plotReadStats)
export(readBedMethyl)
export(readMismatchBam)
export(readModBam)
export(readModkitExtract)
export(refargToDNAStringSet)
export(regionStringToGRanges)
export(regroupReads)
export(regroupReadsByColData)
export(removeAllNAReads)
export(sampleEntropy)
export(subsetReads)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,"rownames<-")
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,as.list)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,ncol)
importFrom(BiocGenerics,nrow)
importFrom(BiocGenerics,pos)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unstrand)
importFrom(BiocParallel,"bpworkers<-")
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpoptions)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNA_BASES)
importFrom(Biostrings,IUPAC_CODE_MAP)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,vcountPattern)
importFrom(Biostrings,vmatchPattern)
importFrom(GenomicRanges,GPos)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,match)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,trim)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,countOverlaps)
importFrom(IRanges,end)
importFrom(IRanges,resize)
importFrom(IRanges,start)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,width)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,make_zero_col_DFrame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(Seqinfo,"seqlengths<-")
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqlevelsInUse)
importFrom(Seqinfo,seqnames)
importFrom(SparseArray,"nnavals<-")
importFrom(SparseArray,NaArray)
importFrom(SparseArray,SVT_SparseArray)
importFrom(SparseArray,colSums)
importFrom(SparseArray,is_nonna)
importFrom(SparseArray,nnavals)
importFrom(SparseArray,nnawhich)
importFrom(SparseArray,pmax)
importFrom(SparseArray,rowSums)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,colnames)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(cli,cli_abort)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_progress_done)
importFrom(cli,cli_progress_step)
importFrom(cli,cli_warn)
importFrom(data.table,fread)
importFrom(dplyr,between)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarize)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,theme_bw)
importFrom(methods,as)
importFrom(methods,is)
importFrom(rlang,.data)
importFrom(stats,IQR)
importFrom(stats,acf)
importFrom(stats,coef)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.pass)
importFrom(stats,pacf)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(utils,modifyList)
importFrom(utils,strcapture)
useDynLib(SingleMoleculeGenomicsIO, .registration = TRUE)