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Defines efficient list-like classes for\nstoring, transforming and aggregating large grouped data, i.e.,\ncollections of atomic vectors and DataFrames.", "biocViews": "Infrastructure, DataRepresentation", "URL": "https://bioconductor.org/packages/IRanges", "BugReports": "https://github.com/Bioconductor/IRanges/issues", "Version": "2.47.5", "License": "Artistic-2.0", "Encoding": "UTF-8", "Authors@R": "c(\nperson(\"Hervé\", \"Pagès\", role=c(\"aut\", \"cre\"),\nemail=\"hpages.on.github@gmail.com\"),\nperson(\"Patrick\", \"Aboyoun\", role=\"aut\"),\nperson(\"Michael\", \"Lawrence\", role=\"aut\"))", "Collate": "thread-control.R range-squeezers.R Vector-class-leftovers.R\nDataFrameList-class.R DataFrameList-utils.R AtomicList-class.R\nAtomicList-utils.R Ranges-and-RangesList-classes.R\nIPosRanges-class.R IPosRanges-comparison.R\nIntegerRangesList-class.R IRanges-class.R IRanges-constructor.R\nmakeIRangesFromDataFrame.R IRanges-utils.R\nRle-class-leftovers.R IPos-class.R 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"toupper,CompressedCharacterList-method", "toupper,CompressedRleList-method", "toupper,SimpleCharacterList-method", "toupper,SimpleRleList-method", "unstrsplit,CharacterList-method", "unstrsplit,RleList-method", "which,CompressedLogicalList-method", "which,CompressedRleList-method", "which,SimpleLogicalList-method", "which,SimpleRleList-method", "which.max,CompressedRleList-method", "which.max,IntegerList-method", "which.max,NumericList-method", "which.max,RleList-method", "which.min,CompressedRleList-method", "which.min,IntegerList-method", "which.min,NumericList-method", "which.min,RleList-method" ] }, { "page": "CompressedHitsList-class", "title": "CompressedHitsList objects", "topics": [ "as.matrix,CompressedHitsList-method", "class:CompressedHitsList", "CompressedHitsList", "CompressedHitsList-class", "from,CompressedHitsList-method", "nLnode,CompressedHitsList-method", "nRnode,CompressedHitsList-method", "space,CompressedHitsList-method", "to,CompressedHitsList-method" ] }, { "page": "CompressedList-class", "title": "CompressedList objects", "topics": [ "!,CompressedList-method", "bindROWS,CompressedList-method", "class:CompressedList", "classNameForDisplay,CompressedList-method", "coerce,ANY,CompressedList-method", "CompressedList", "CompressedList-class", "elementNROWS,CompressedList-method", "is.na,CompressedList-method", "lapply,CompressedList-method", "length,CompressedList-method", "match,CompressedList,vector-method", "names,CompressedList-method", "names<-,CompressedList-method", "revElements,CompressedList-method", "unlist,CompressedList-method" ] }, { "page": "coverage-methods", "title": "Coverage of a set of ranges", "topics": [ "coverage", "coverage,IntegerRanges-method", "coverage,IntegerRangesList-method", "coverage,StitchedIPos-method", "coverage,Views-method", "coverage-methods" ] }, { "page": "DataFrameList-class", "title": "List of DataFrames", "topics": [ "as.env,SDFLWrapperForTransform-method", "cbind,DataFrameList-method", "class:CompressedDataFrameList", "class:CompressedDFrameList", "class:CompressedSplitDataFrameList", "class:CompressedSplitDFrameList", "class:DataFrameList", "class:DFrameList", "class:SimpleDataFrameList", "class:SimpleDFrameList", "class:SimpleSplitDataFrameList", "class:SimpleSplitDFrameList", "class:SplitDataFrameList", "class:SplitDFrameList", "classNameForDisplay,CompressedDFrameList-method", "classNameForDisplay,SimpleDFrameList-method", "coerce,ANY,CompressedDataFrameList-method", "coerce,ANY,CompressedSplitDataFrameList-method", "coerce,ANY,CompressedSplitDFrameList-method", "coerce,ANY,DataFrameList-method", "coerce,ANY,SimpleDataFrameList-method", "coerce,ANY,SimpleSplitDataFrameList-method", "coerce,ANY,SimpleSplitDFrameList-method", "coerce,ANY,SplitDataFrameList-method", "coerce,ANY,SplitDFrameList-method", "coerce,DataFrame,SplitDFrameList-method", "coerce,DataFrameList,DFrame-method", "coerce,List,CompressedSplitDFrameList-method", "coerce,List,SimpleSplitDFrameList-method", "coerce,list,SplitDFrameList-method", "coerce,SimpleList,SplitDFrameList-method", "coerce,SplitDataFrameList,DFrame-method", "colnames,CompressedSplitDataFrameList-method", "colnames,DataFrameList-method", "colnames,SDFLWrapperForTransform-method", "colnames,SplitDataFrameList-method", "colnames<-,CompressedSplitDataFrameList-method", "colnames<-,SimpleDataFrameList-method", "columnMetadata", "columnMetadata,CompressedSplitDataFrameList-method", "columnMetadata,SimpleSplitDataFrameList-method", "columnMetadata<-", "columnMetadata<-,CompressedSplitDataFrameList-method", "columnMetadata<-,SimpleSplitDataFrameList-method", "commonColnames", "commonColnames,CompressedSplitDataFrameList-method", "commonColnames,SimpleSplitDataFrameList-method", "commonColnames<-", "commonColnames<-,CompressedSplitDataFrameList-method", "commonColnames<-,SimpleSplitDataFrameList-method", "CompressedDataFrameList", "CompressedDataFrameList-class", "CompressedDFrameList", "CompressedDFrameList-class", "CompressedSplitDataFrameList", "CompressedSplitDataFrameList-class", "CompressedSplitDFrameList", "CompressedSplitDFrameList-class", "DataFrameList", "DataFrameList-class", "DFrameList", "DFrameList-class", "dim,DataFrameList-method", "dimnames,DataFrameList-method", "dimnames<-,DataFrameList-method", "dims,DataFrameList-method", "ncol,CompressedSplitDataFrameList-method", "ncol,DataFrameList-method", "ncol,SimpleSplitDataFrameList-method", "ncols,CompressedSplitDataFrameList-method", "ncols,DataFrameList-method", "ncols,SimpleSplitDataFrameList-method", "NROW,DataFrameList-method", "nrow,DataFrameList-method", "nrows,DataFrameList-method", "rbind,DataFrameList-method", "ROWNAMES,DataFrameList-method", "rownames,DataFrameList-method", "rownames<-,CompressedSplitDataFrameList-method", "ROWNAMES<-,DataFrameList-method", "rownames<-,SimpleDataFrameList-method", "show,SplitDataFrameList-method", "SimpleDataFrameList", "SimpleDataFrameList-class", "SimpleDFrameList", "SimpleDFrameList-class", "SimpleSplitDataFrameList", "SimpleSplitDataFrameList-class", "SimpleSplitDFrameList", "SimpleSplitDFrameList-class", "SplitDataFrameList", "SplitDataFrameList-class", "SplitDFrameList", "SplitDFrameList-class", "stack,DataFrameList-method", "transform,SplitDataFrameList-method", "[,CompressedSplitDataFrameList-method", "[,SimpleSplitDataFrameList-method", "[<-,SplitDataFrameList-method", "[[,SDFLWrapperForTransform-method", "[[<-,SDFLWrapperForTransform-method" ] }, { "page": "extractList", "title": "Group elements of a vector-like object into a list-like object", "topics": [ "extractList", "extractList,ANY,ANY-method", "extractList,ANY-method", "regroup", "relist", "relist,ANY,List-method", "relist,ANY,PartitioningByEnd-method", "relist,Vector,list-method" ] }, { "page": "extractListFragments", "title": "Extract list fragments from a list-like object", "topics": [ "equisplit", "extractListFragments", "INCOMPATIBLE_ARANGES_MSG" ] }, { "page": "findOverlaps-methods", "title": "Finding overlapping ranges", "topics": [ "%outside%", "%over%", "%within%", "countOverlaps", "countOverlaps,integer,Vector-method", "countOverlaps,IntegerRanges,IntegerRanges-method", "countOverlaps,IntegerRangesList,IntegerRangesList-method", "countOverlaps,Vector,missing-method", "countOverlaps,Vector,Vector-method", "findOverlapPairs", "findOverlaps", "findOverlaps,ANY,Pairs-method", "findOverlaps,integer,IntegerRanges-method", "findOverlaps,IntegerRanges,IntegerRanges-method", "findOverlaps,IntegerRangesList,IntegerRangesList-method", "findOverlaps,Pairs,ANY-method", "findOverlaps,Pairs,missing-method", "findOverlaps,Pairs,Pairs-method", "findOverlaps,Vector,missing-method", "findOverlaps-methods", "mergeByOverlaps", "overlapsAny", "overlapsAny,integer,Vector-method", "overlapsAny,IntegerRangesList,IntegerRangesList-method", "overlapsAny,Vector,missing-method", "overlapsAny,Vector,Vector-method", "overlapsRanges", "overlapsRanges,IntegerRanges,IntegerRanges-method", "overlapsRanges,IntegerRangesList,IntegerRangesList-method", "poverlaps", "poverlaps,integer,IntegerRanges-method", "poverlaps,IntegerRanges,integer-method", "poverlaps,IntegerRanges,IntegerRanges-method", "subsetByOverlaps", "subsetByOverlaps,Vector,Vector-method" ] }, { "page": "Grouping-class", "title": "Grouping objects", "topics": [ "bindROWS,Partitioning-method", "class:CompressedGrouping", "class:CompressedManyToManyGrouping", "class:CompressedManyToOneGrouping", "class:Dups", "class:Grouping", "class:GroupingIRanges", "class:GroupingRanges", "class:H2LGrouping", "class:ManyToManyGrouping", "class:ManyToOneGrouping", "class:Partitioning", "class:PartitioningByEnd", "class:PartitioningByWidth", "class:PartitioningMap", "class:SimpleGrouping", "class:SimpleManyToManyGrouping", "class:SimpleManyToOneGrouping", "coerce,DataFrame,Grouping-method", "coerce,FactorList,Grouping-method", "coerce,grouping,Grouping-method", "coerce,grouping,ManyToOneGrouping-method", "coerce,Hits,Grouping-method", "coerce,IntegerRanges,PartitioningByEnd-method", "coerce,IntegerRanges,PartitioningByWidth-method", "coerce,ManyToOneGrouping,factor-method", "coerce,vector,Grouping-method", "coerce,vector,ManyToManyGrouping-method", "coerce,vector,ManyToOneGrouping-method", "CompressedGrouping-class", "CompressedManyToManyGrouping-class", "CompressedManyToOneGrouping-class", "duplicated,Dups-method", "Dups", "Dups-class", "end,PartitioningByEnd-method", "end,PartitioningByWidth-method", "extractROWS,Partitioning-method", "Grouping", "Grouping-class", "GroupingIRanges", "GroupingIRanges-class", "GroupingRanges", "GroupingRanges-class", "grouplengths", "grouplengths,CompressedGrouping-method", "grouplengths,Grouping-method", "grouplengths,GroupingRanges-method", "grouplengths,H2LGrouping-method", "grouprank", "grouprank,H2LGrouping-method", "H2LGrouping", "H2LGrouping-class", "high2low", "high2low,ANY-method", "high2low,H2LGrouping-method", "length,H2LGrouping-method", "length,PartitioningByEnd-method", "length,PartitioningByWidth-method", "length<-,H2LGrouping-method", "low2high", "low2high,H2LGrouping-method", "ManyToManyGrouping", "ManyToManyGrouping-class", "ManyToOneGrouping", "ManyToOneGrouping-class", "mapOrder", "mapOrder,PartitioningMap-method", "members", "members,H2LGrouping-method", "members,ManyToOneGrouping-method", "names,Partitioning-method", "names<-,Partitioning-method", "nobj", "nobj,BaseManyToManyGrouping-method", "nobj,CompressedManyToOneGrouping-method", "nobj,H2LGrouping-method", "nobj,ManyToManyGrouping-method", "nobj,ManyToOneGrouping-method", "nobj,PartitioningByEnd-method", "parallel_slot_names,Partitioning-method", "parallel_slot_names,PartitioningByEnd-method", "parallel_slot_names,PartitioningByWidth-method", "Partitioning", "Partitioning-class", "PartitioningByEnd", "PartitioningByEnd-class", "PartitioningByWidth", "PartitioningByWidth-class", "PartitioningMap", "PartitioningMap-class", "show,Dups-method", "show,Grouping-method", "show,PartitioningMap-method", "SimpleGrouping-class", "SimpleManyToManyGrouping-class", "SimpleManyToOneGrouping-class", "start,PartitioningByEnd-method", "start,PartitioningByWidth-method", "togroup", "togroup,ANY-method", "togroup,H2LGrouping-method", "togroup,ManyToOneGrouping-method", "togroup,Partitioning-method", "togrouplength", "togrouplength,ManyToOneGrouping-method", "togrouprank", "togrouprank,H2LGrouping-method", "vmembers", "vmembers,H2LGrouping-method", "vmembers,ManyToOneGrouping-method", "width,PartitioningByEnd-method", "width,PartitioningByWidth-method" ] }, { "page": "Hits-class-leftovers", "title": "Examples of basic manipulation of Hits objects", "topics": [ "as.list,Hits-method", "as.list,SortedByQueryHits-method", "coerce,Hits,CompressedIntegerList-method", "coerce,Hits,Grouping", "coerce,Hits,IntegerList-method", "coerce,Hits,List-method", "coerce,SortedByQueryHits,CompressedIntegerList-method", "coerce,SortedByQueryHits,IntegerList-method", "coerce,SortedByQueryHits,IntegerRanges-method", "coerce,SortedByQueryHits,IRanges-method", "coerce,SortedByQueryHits,List-method", "coerce,SortedByQueryHits,Partitioning-method", "coerce,SortedByQueryHits,PartitioningByEnd-method", "Hits-examples" ] }, { "page": "IntegerRanges-class", "title": "IntegerRanges objects", "topics": [ "class:IntegerRanges", "IntegerRanges", "IntegerRanges-class" ] }, { "page": "IntegerRangesList-class", "title": "IntegerRangesList objects", "topics": [ "class:IntegerRangesList", "class:SimpleIntegerRangesList", "end,RangesList-method", "end<-,IntegerRangesList-method", "IntegerRangesList", "IntegerRangesList-class", "isNormal,IntegerRangesList-method", "merge,IntegerRangesList,IntegerRangesList-method", "merge,IntegerRangesList,missing-method", "merge,missing,IntegerRangesList-method", "pos,PosList-method", "show,IntegerRangesList-method", "SimpleIntegerRangesList", "SimpleIntegerRangesList-class", "space", "space,IntegerRangesList-method", "start,RangesList-method", "start<-,IntegerRangesList-method", "whichFirstNotNormal,IntegerRangesList-method", "width,RangesList-method", "width<-,IntegerRangesList-method" ] }, { "page": "inter-range-methods", "title": "Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object", "topics": [ "disjoin", "disjoin,CompressedIRangesList-method", "disjoin,IntegerRanges-method", "disjoin,IntegerRangesList-method", "disjoin,NormalIRanges-method", "disjointBins", "disjointBins,IntegerRanges-method", "disjointBins,IntegerRangesList-method", "disjointBins,NormalIRanges-method", "gaps", "gaps,CompressedIRangesList-method", "gaps,IntegerRanges-method", "gaps,IntegerRangesList-method", "gaps,MaskCollection-method", "gaps,Views-method", "inter-range-methods", "isDisjoint", "isDisjoint,IntegerRanges-method", "isDisjoint,IntegerRangesList-method", "isDisjoint,NormalIRanges-method", "isDisjoint,StitchedIPos-method", "range", "range,CompressedIRangesList-method", "range,IntegerRanges-method", "range,IntegerRangesList-method", "range,StitchedIPos-method", "reduce", "reduce,CompressedIRangesList-method", "reduce,IntegerRanges-method", "reduce,IntegerRangesList-method", "reduce,Views-method" ] }, { "page": "intra-range-methods", "title": "Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object", "topics": [ "flank", "flank,Ranges-method", "flank,RangesList-method", "intra-range-methods", "narrow", "narrow,ANY-method", "narrow,MaskCollection-method", "Ops,CompressedRangesList,numeric-method", "Ops,Ranges,numeric-method", "Ops,RangesList,numeric-method", "promoters", "promoters,IntegerRanges-method", "promoters,RangesList-method", "reflect", "reflect,IntegerRanges-method", "resize", "resize,Ranges-method", "resize,RangesList-method", "restrict", "restrict,IntegerRanges-method", "restrict,RangesList-method", "restrict,Views-method", "shift", "shift,IPos-method", "shift,Ranges-method", "shift,RangesList-method", "terminators", "terminators,IntegerRanges-method", "terminators,RangesList-method", "threebands", "threebands,IRanges-method", "update_ranges", "update_ranges,IRanges-method", "update_ranges,Views-method", "windows,Ranges-method" ] }, { "page": "IPos-class", "title": "IPos objects", "topics": [ "as.data.frame,IPos-method", "as.data.frame.IPos", "bindROWS,IPos-method", "class:IPos", "class:StitchedIPos", "class:UnstitchedIPos", "coerce,ANY,IPos-method", "coerce,ANY,StitchedIPos-method", "coerce,ANY,UnstitchedIPos-method", "coerce,IntegerRanges,IPos-method", "coerce,IntegerRanges,StitchedIPos-method", "coerce,IntegerRanges,UnstitchedIPos-method", "coerce,StitchedIPos,UnstitchedIPos-method", "coerce,UnstitchedIPos,StitchedIPos-method", "extractROWS,IPos-method", "IPos", "IPos-class", "length,IPos-method", "length,UnstitchedIPos-method", "names,IPos-method", "names<-,IPos-method", "parallel_slot_names,IPos-method", "parallel_slot_names,UnstitchedIPos-method", "pos", "pos,IPos-method", "pos,UnstitchedIPos-method", "show,IPos-method", "StitchedIPos", "StitchedIPos-class", "summary,IPos-method", "summary.IPos", "UnstitchedIPos", "UnstitchedIPos-class", "updateObject,IPos-method" ] }, { "page": "IPosRanges-class", "title": "IPosRanges objects", "topics": [ "as.character,IPosRanges-method", "as.data.frame,IPosRanges-method", "as.data.frame.IPosRanges", "as.factor,IPosRanges-method", "as.matrix,IPosRanges-method", "class:IPosRanges", "elementNROWS,Ranges-method", "end,Pos-method", "end,Ranges-method", "end<-", "getListElement,IPosRanges-method", "IPosRanges", "IPosRanges-class", "isEmpty,Ranges-method", "isNormal", "isNormal,Ranges-method", "length,Ranges-method", "mid", "mid,Ranges-method", "show,IPosRanges-method", "slidingWindows", "slidingWindows,IPosRanges-method", "start,Pos-method", "start,Ranges-method", "start<-", "summary,IPosRanges-method", "summary.IPosRanges", "tile", "tile,IPosRanges-method", "whichFirstNotNormal", "whichFirstNotNormal,Ranges-method", "width", "width,Pos-method", "width,Ranges-method", "width<-" ] }, { "page": "IPosRanges-comparison", "title": "Comparing and ordering ranges", "topics": [ "IPosRanges-comparison", "is.unsorted,IPosRanges-method", "match,IPosRanges,IPosRanges-method", "order,IPosRanges-method", "pcompare", "pcompare,IPosRanges,IPosRanges-method", "rangeComparisonCodeToLetter", "selfmatch,IPosRanges-method" ] }, { "page": "IRanges-class", "title": "IRanges and NormalIRanges objects", "topics": [ "class:IRanges", "class:NormalIRanges", "coerce,ANY,IntegerRanges-method", "coerce,character,IRanges-method", "coerce,factor,IRanges-method", "coerce,integer,IRanges-method", "coerce,integer,NormalIRanges-method", "coerce,IntegerRanges,IRanges-method", "coerce,logical,IRanges-method", "coerce,logical,NormalIRanges-method", "coerce,numeric,IRanges-method", "coerce,numeric,NormalIRanges-method", "end<-,IRanges-method", "IRanges-class", "isEmpty,NormalIRanges-method", "isNormal,IRanges-method", "isNormal,NormalIRanges-method", "max,NormalIRanges-method", "min,NormalIRanges-method", "names,IRanges-method", "names<-,IRanges-method", "NormalIRanges", "NormalIRanges-class", "parallel_slot_names,IRanges-method", "ranges,IntegerRanges-method", "start,IRanges-method", "start<-,IRanges-method", "width,IRanges-method", "width<-,IRanges-method" ] }, { "page": "IRanges-constructor", "title": "The IRanges constructor and supporting functions", "topics": [ "IRanges", "IRanges-constructor", "solveUserSEW" ] }, { "page": "IRanges-utils", "title": "IRanges utility functions", "topics": [ "asNormalIRanges", "breakInChunks", "coerce,IRanges,NormalIRanges-method", "IRanges-utils", "successiveIRanges", "whichAsIRanges" ] }, { "page": "IRangesList-class", "title": "List of IRanges and NormalIRanges", "topics": [ "as.list,CompressedNormalIRangesList-method", "class:CompressedIRangesList", "class:CompressedNormalIRangesList", "class:IRangesList", "class:NormalIRangesList", "class:SimpleIRangesList", "class:SimpleNormalIRangesList", "coerce,CompressedIRangesList,CompressedNormalIRangesList-method", "coerce,CompressedRleList,CompressedIRangesList-method", "coerce,IntegerRanges,CompressedIRangesList-method", "coerce,IntegerRangesList,CompressedNormalIRangesList-method", "coerce,IntegerRangesList,NormalIRangesList-method", "coerce,IntegerRangesList,SimpleIRangesList-method", "coerce,IntegerRangesList,SimpleNormalIRangesList-method", "coerce,List,CompressedIRangesList-method", "coerce,list,CompressedIRangesList-method", "coerce,List,IRangesList-method", "coerce,list,IRangesList-method", "coerce,List,SimpleIRangesList-method", "coerce,list,SimpleIRangesList-method", "coerce,LogicalList,CompressedNormalIRangesList-method", "coerce,LogicalList,NormalIRangesList-method", "coerce,LogicalList,SimpleNormalIRangesList-method", "coerce,NormalIRangesList,CompressedNormalIRangesList-method", "coerce,RleList,CompressedNormalIRangesList-method", "coerce,RleList,NormalIRangesList-method", "coerce,RleList,SimpleNormalIRangesList-method", "coerce,SimpleIntegerRangesList,SimpleIRangesList-method", "coerce,SimpleIRangesList,SimpleNormalIRangesList-method", "coerce,SimpleList,SimpleIRangesList-method", "CompressedIRangesList", "CompressedIRangesList-class", "CompressedNormalIRangesList", "CompressedNormalIRangesList-class", "end,CompressedRangesList-method", "IRangesList", "IRangesList-class", "isNormal,CompressedIRangesList-method", "isNormal,SimpleIRangesList-method", "max,CompressedNormalIRangesList-method", "max,SimpleNormalIRangesList-method", "min,CompressedNormalIRangesList-method", "min,SimpleNormalIRangesList-method", "NormalIRangesList", "NormalIRangesList-class", "pos,CompressedPosList-method", "SimpleIRangesList", "SimpleIRangesList-class", "SimpleNormalIRangesList", "SimpleNormalIRangesList-class", "start,CompressedRangesList-method", "summary,CompressedIRangesList-method", "unlist,SimpleNormalIRangesList-method", "width,CompressedRangesList-method" ] }, { "page": "makeIRangesFromDataFrame", "title": "Make a IRanges object from a data.frame or DataFrame", "topics": [ "coerce,data.frame,IRanges-method", "coerce,DataFrame,IRanges-method", "makeIRangesFromDataFrame" ] }, { "page": "MaskCollection-class", "title": "MaskCollection objects", "topics": [ "active", "active,MaskCollection-method", "active<-", "active<-,MaskCollection-method", "append,MaskCollection,MaskCollection-method", "class:MaskCollection", "coerce,MaskCollection,NormalIRanges-method", "collapse", "collapse,MaskCollection-method", "desc", "desc,MaskCollection-method", "desc<-", "desc<-,MaskCollection-method", "length,MaskCollection-method", "Mask", "MaskCollection", "MaskCollection-class", "MaskCollection.show_frame", "maskedratio", "maskedratio,MaskCollection-method", "maskedwidth", "maskedwidth,MaskCollection-method", "max,MaskCollection-method", "min,MaskCollection-method", "names,MaskCollection-method", "names<-,MaskCollection-method", "nir_list", "nir_list,MaskCollection-method", "show,MaskCollection-method", "width,MaskCollection-method" ] }, { "page": "multisplit", "title": "Split elements belonging to multiple groups", "topics": [ "multisplit" ] }, { "page": "NCList-class", "title": "Nested Containment List objects", "topics": [ "bindROWS,NCList-method", "class:NCList", "class:NCLists", "coerce,IntegerRanges,NCList-method", "coerce,IntegerRangesList,NCLists-method", "coerce,NCLists,CompressedIRangesList-method", "coerce,NCLists,IRangesList-method", "elementNROWS,NCLists-method", "end,NCList-method", "end,NCLists-method", "extractROWS,NCList,ANY-method", "length,NCList-method", "length,NCLists-method", "names,NCList-method", "names,NCLists-method", "NCList", "NCList-class", "NCLists", "NCLists-class", "parallel_slot_names,NCLists-method", "ranges,NCLists-method", "start,NCList-method", "start,NCLists-method", "width,NCList-method", "width,NCLists-method" ] }, { "page": "nearest-methods", "title": "Finding the nearest range/position neighbor", "topics": [ "class:IntegerRanges_OR_missing", "distance", "distance,IntegerRanges,IntegerRanges-method", "distance,Pairs,missing-method", "distanceToNearest", "distanceToNearest,IntegerRanges,IntegerRanges_OR_missing-method", "follow", "follow,IntegerRanges,IntegerRanges_OR_missing-method", "IntegerRanges_OR_missing", "IntegerRanges_OR_missing-class", "nearest", "nearest,IntegerRanges,IntegerRanges_OR_missing-method", "nearest-methods", "precede", "precede,IntegerRanges,IntegerRanges_OR_missing-method", "selectNearest" ] }, { "page": "range-squeezers", "title": "Squeeze the ranges out of a range-based object", "topics": [ "range-squeezers", "ranges", "rglist", "rglist,Pairs-method" ] }, { "page": "RangedSelection-class", "title": "Selection of ranges and columns", "topics": [ "coerce,IntegerRangesList,RangedSelection-method", "colnames,RangedSelection-method", "colnames<-,RangedSelection-method", "RangedSelection", "RangedSelection-class", "ranges,RangedSelection-method", "ranges<-,RangedSelection-method" ] }, { "page": "read.Mask", "title": "Read a mask from a file", "topics": [ "read.agpMask", "read.gapMask", "read.liftMask", "read.Mask", "read.rmMask", "read.trfMask" ] }, { "page": "reverse-methods", "title": "reverse", "topics": [ "reverse", "reverse,character-method", "reverse,IRanges-method", "reverse,MaskCollection-method", "reverse,NormalIRanges-method", "reverse,Views-method" ] }, { "page": "Rle-class-leftovers", "title": "Rle objects (old man page)", "topics": [ "coerce,Rle,IRanges-method", "coerce,Rle,NormalIRanges-method", "findRange", "findRange,Rle-method", "ranges,Rle-method", "splitRanges", "splitRanges,Rle-method", "splitRanges,vector_OR_factor-method" ] }, { "page": "RleViews-class", "title": "The RleViews class", "topics": [ "class:RleViews", "RleViews", "RleViews-class", "show,RleViews-method", "Views,Rle-method" ] }, { "page": "RleViewsList-class", "title": "List of RleViews", "topics": [ "coerce,RleViewsList,IRangesList-method", "coerce,RleViewsList,SimpleIRangesList-method", "RleViewsList", "RleViewsList-class", "SimpleRleViewsList-class", "subject,SimpleRleViewsList-method", "Views,RleList-method" ] }, { "page": "seqapply", "title": "2 methods that should be documented somewhere else", "topics": [ "split<-,Vector-method", "unsplit,List-method" ] }, { "page": "setops-methods", "title": "Set operations on IntegerRanges and IntegerRangesList objects", "topics": [ "intersect", "intersect,CompressedIRangesList,CompressedIRangesList-method", "intersect,IntegerRanges,IntegerRanges-method", "intersect,IntegerRangesList,IntegerRangesList-method", "intersect,Pairs,missing-method", "pgap", "pgap,IntegerRanges,IntegerRanges-method", "pintersect", "pintersect,IntegerRanges,IntegerRanges-method", 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