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255 lines (254 loc) · 7.6 KB
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# Generated by roxygen2: do not edit by hand
export(addFootprints)
export(addReadStats)
export(addSeqContext)
export(calcAndCountDist)
export(calcFootprintScores)
export(calcModbaseSpacing)
export(calcReadStats)
export(countStatePairs)
export(estimateNRL)
export(estimateNRLwindows)
export(estimateNoiseParsWindows)
export(estimateSNRwindows)
export(extractSeqContext)
export(filterPositions)
export(filterReads)
export(filterReadsBam)
export(flattenReadLevelAssay)
export(getAnchorRegions)
export(getDifferentialWindows)
export(getDifferentiallyModifiedWindows)
export(getRangesWithAssayValues)
export(phasingScoreFourier)
export(plotBigWig)
export(plotGenomicRegions)
export(plotModbaseSpacing)
export(plotNoisePars)
export(plotReadStats)
export(plotReadsHeatmap)
export(plotReadsLollipop)
export(plotRegion)
export(plotSummaryPointSmooth)
export(plotValsBySeqContext)
export(processWindowScores)
export(quantifyWindowsInRegion)
export(readBedMethyl)
export(readModBam)
export(readModkitExtract)
export(regroupReads)
export(regroupReadsByColData)
export(sampleEntropy)
export(scanForHighScoringRegions)
export(segmentFootprintScores)
export(strandDiffFracMod)
export(subsetReads)
export(sumNmodNvalid)
importFrom(BSgenome,getSeq)
importFrom(BiocGenerics,"rownames<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,as.list)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,intersect)
importFrom(BiocGenerics,ncol)
importFrom(BiocGenerics,nrow)
importFrom(BiocGenerics,pos)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,setdiff)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,unlist)
importFrom(BiocParallel,"bpworkers<-")
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpoptions)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,vcountPattern)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GPos)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,match)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,shift)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,trim)
importFrom(IRanges,DataFrameList)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,Views)
importFrom(IRanges,coerce)
importFrom(IRanges,disjointBins)
importFrom(IRanges,end)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,ranges)
importFrom(IRanges,reduce)
importFrom(IRanges,resize)
importFrom(IRanges,start)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,viewApply)
importFrom(IRanges,viewWhichMaxs)
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(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(SparseArray,"nnavals<-")
importFrom(SparseArray,NaArray)
importFrom(SparseArray,SVT_SparseArray)
importFrom(SparseArray,cbind)
importFrom(SparseArray,colMeans)
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,ncol)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(SummarizedExperiment,start)
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,across)
importFrom(dplyr,all_of)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_modify)
importFrom(dplyr,group_split)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(ggforce,facet_col)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_c)
importFrom(ggplot2,scale_linewidth_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(grDevices,colorRampPalette)
importFrom(methods,as)
importFrom(methods,is)
importFrom(patchwork,wrap_plots)
importFrom(rlang,.data)
importFrom(scales,label_number)
importFrom(scales,squish)
importFrom(stats,IQR)
importFrom(stats,acf)
importFrom(stats,as.dist)
importFrom(stats,chisq.test)
importFrom(stats,coef)
importFrom(stats,coefficients)
importFrom(stats,complete.cases)
importFrom(stats,confint)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.pass)
importFrom(stats,pacf)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,residuals)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,smooth.spline)
importFrom(stats,summary.lm)
importFrom(stats,var)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(tidytext,reorder_within)
importFrom(tidytext,scale_x_reordered)
importFrom(utils,modifyList)
importFrom(utils,strcapture)
importFrom(zoo,na.approx)
importFrom(zoo,rollmean)
useDynLib(footprintR, .registration = TRUE)