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NAMESPACE
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160 lines (159 loc) · 4.43 KB
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# Generated by roxygen2: do not edit by hand
export(ChromatinContacts)
export(MultiWayContacts)
export(calcGenomeCovChunked)
export(calcResDepthChunked)
export(calculateGenomeCoverage)
export(calculateResolutionDepth)
export(concatemers2Gis)
export(findOptResChunked)
export(findOptimalResolution)
export(geom_annotation)
export(geom_concatemer)
export(geom_concatemer2)
export(geom_hic)
export(geom_hic_under)
export(geom_hypergraph)
export(geom_ideogram)
export(geom_loop)
export(geom_loop2)
export(geom_tad)
export(geom_tad2)
export(geom_track)
export(geom_track2)
export(getBreaksLabels)
export(plotCoverageCurve)
export(plotResolutionCoverage)
export(readPairsCache)
export(renameGeomAes)
export(scaleData)
export(theme_hic)
exportClasses(ChromatinContacts)
exportClasses(MultiWayContacts)
exportMethods("[")
exportMethods("features<-")
exportMethods(as_tibble)
exportMethods(build)
exportMethods(features)
exportMethods(focus)
exportMethods(gghic)
exportMethods(gghypergraph)
exportMethods(hypergraphData)
exportMethods(import)
exportMethods(interactions)
exportMethods(resolution)
exportMethods(select)
exportMethods(seqinfo)
exportMethods(subsetByOverlaps)
exportMethods(tidy)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(InteractionSet,GInteractions)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(S4Vectors,SimpleList)
importClassesFrom(Seqinfo,Seqinfo)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,pintersect)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqinfo)
importFrom(GenomicRanges,split)
importFrom(GenomicRanges,start)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,subsetByOverlaps)
importFrom(InteractionSet,"replaceRegions<-")
importFrom(InteractionSet,GInteractions)
importFrom(InteractionSet,anchors)
importFrom(InteractionSet,interactions)
importFrom(InteractionSet,pairdist)
importFrom(InteractionSet,regions)
importFrom(InteractionSet,swapAnchors)
importFrom(Matrix,colSums)
importFrom(Matrix,nnzero)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,summary)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,reframe)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,slice_max)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(ggplot2,"%+replace%")
importFrom(ggplot2,Geom)
importFrom(ggplot2,Stat)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,draw_key_blank)
importFrom(ggplot2,draw_key_path)
importFrom(ggplot2,draw_key_polygon)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,ggproto_parent)
importFrom(ggplot2,layer)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(grDevices,colorRampPalette)
importFrom(grid,arrow)
importFrom(grid,gList)
importFrom(grid,gpar)
importFrom(grid,is.unit)
importFrom(grid,nullGrob)
importFrom(grid,pathGrob)
importFrom(grid,pointsGrob)
importFrom(grid,polygonGrob)
importFrom(grid,polylineGrob)
importFrom(grid,segmentsGrob)
importFrom(grid,textGrob)
importFrom(grid,unit)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,show)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_df)
importFrom(purrr,pmap)
importFrom(rhdf5,h5read)
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,sym)
importFrom(rtracklayer,browserSession)
importFrom(rtracklayer,genome)
importFrom(rtracklayer,getTable)
importFrom(rtracklayer,import)
importFrom(rtracklayer,ucscTableQuery)
importFrom(scales,oob_squish)
importFrom(scales,percent)
importFrom(scales,unit_format)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,drop_na)
importFrom(tidyr,replace_na)
importFrom(utils,globalVariables)
useDynLib(gghic, .registration = TRUE)