Package: IRanges 2.39.1

Hervé Pagès

IRanges: Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Authors:Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut]

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NEWS

# Install 'IRanges' in R:

install.packages('IRanges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/iranges/issues

On BioConductor:IRanges-2.39.0(bioc 3.20)IRanges-2.38.0(bioc 3.19)

bioconductor-package

256 exports 13.90 score 2 dependencies 1716 dependents 62 mentions

Last updated 7 days agofrom:1b189a464a

Exports:%outside%%over%%poutside%%pover%%pwithin%%within%active active<-anyDuplicated append as.data.frame as.data.frame.IPos as.data.frame.IPosRanges as.env as.factor as.list as.matrix asNormalIRanges bindROWS breakInChunks by cbind CharacterList chartr classNameForDisplay coerce collapse colnames colnames<-columnMetadata columnMetadata<-commonColnames commonColnames<-Complex ComplexList cor countOverlaps cov coverage cvg DataFrameList desc desc<-diff diff.AtomicList dims disjoin disjointBins distance distanceToNearest drop duplicated Dups elementNROWS end end<-endsWith equisplit extractList extractListFragments extractROWS FactorList findOverlapPairs findOverlaps findRange flank follow from gaps getListElement grouplengths grouprank gsub H2LGrouping heads high2low ifelse2 INCOMPATIBLE_ARANGES_MSG IntegerList intersect IPos IQR IRanges IRangesList is.unsorted isDisjoint isEmpty isNormal lapply LogicalList low2high mad ManyToManyGrouping ManyToOneGrouping mapOrder Mask MaskCollection.show_frame maskedratio maskedwidth match Math Math2 mean median members merge mergeByOverlaps mid multisplit narrow nchar NCList NCLists ncol NCOL ncols nearest nir_list nLnode nobj nRnode nrow NROW nrows NumericList Ops order overlapsAny overlapsRanges parallel_slot_names PartitioningByEnd PartitioningByWidth PartitioningMap paste pcompare pcompareRecursively pgap pintersect pmax pmax.int pmin pmin.int pos poverlaps precede promoters psetdiff punion quantile rangeComparisonCodeToLetter RangedSelection ranges ranges<-RawList rbind read.agpMask read.gapMask read.liftMask read.rmMask read.trfMask reduce reflect regroup relist replaceROWS resize restrict revElements reverse rglist RleList RleViewsList rownames ROWNAMES rownames<-ROWNAMES<-runLength runmean runmed runq runsum runValue<-runwtsum sd selectNearest selfmatch setdiff shift show slice slidingIRanges slidingViews slidingWindows smoothEnds solveUserSEW space split<-SplitDataFrameList splitRanges stack start start<-startsWith sub subject subsetByOverlaps subviews successiveIRanges successiveViews summary Summary summary.IPos summary.IPosRanges table tails tapply terminators threebands tile to togroup togrouplength togrouprank tolower toupper transform trim union unique unsplit update_ranges updateObject var viewApply viewMaxs viewMeans viewMins viewRangeMaxs viewRangeMins Views viewSums viewWhichMaxs viewWhichMins vmembers which which.max which.min whichAsIRanges whichFirstNotNormal width width<-window<-window<-.factor window<-.vector window<-.Vector windows

Dependencies:BiocGenerics S4Vectors

An Overview of the IRanges package

Rendered fromIRangesOverview.Rnwusingutils::Sweaveon Jul 04 2024.

Last update: 2018-07-17
Started: 2013-10-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Lists of Atomic Vectors in Natural and Rle Form	as.list,CompressedAtomicList-method as.matrix,AtomicList-method as.vector,AtomicList-method AtomicList AtomicList-class CharacterList CharacterList-class class:AtomicList class:CharacterList class:ComplexList class:CompressedAtomicList class:CompressedCharacterList class:CompressedComplexList class:CompressedFactorList class:CompressedIntegerList class:CompressedLogicalList class:CompressedNumericList class:CompressedRawList class:CompressedRleList class:FactorList class:IntegerList class:LogicalList class:NumericList class:RawList class:RleList class:SimpleAtomicList class:SimpleCharacterList class:SimpleComplexList class:SimpleFactorList class:SimpleIntegerList class:SimpleLogicalList class:SimpleNumericList class:SimpleRawList class:SimpleRleList coerce,AtomicList,CharacterList-method coerce,AtomicList,ComplexList-method coerce,AtomicList,IntegerList-method coerce,AtomicList,LogicalList-method coerce,AtomicList,NumericList-method coerce,AtomicList,RawList-method coerce,AtomicList,RleList-method coerce,AtomicList,RleViews coerce,CompressedAtomicList,list-method coerce,vector,AtomicList-method coerce,vector,CompressedCharacterList-method coerce,vector,CompressedComplexList-method coerce,vector,CompressedIntegerList-method coerce,vector,CompressedLogicalList-method coerce,vector,CompressedNumericList-method coerce,vector,CompressedRawList-method coerce,vector,CompressedRleList-method coerce,vector,SimpleCharacterList-method coerce,vector,SimpleComplexList-method coerce,vector,SimpleIntegerList-method coerce,vector,SimpleLogicalList-method coerce,vector,SimpleNumericList-method coerce,vector,SimpleRawList-method coerce,vector,SimpleRleList-method ComplexList ComplexList-class CompressedAtomicList CompressedAtomicList-class CompressedCharacterList CompressedCharacterList-class CompressedComplexList CompressedComplexList-class CompressedFactorList CompressedFactorList-class CompressedIntegerList CompressedIntegerList-class CompressedLogicalList CompressedLogicalList-class CompressedNumericList CompressedNumericList-class CompressedRawList CompressedRawList-class CompressedRleList CompressedRleList-class drop,AtomicList-method duplicated,CompressedAtomicList-method duplicated,CompressedList-method FactorList FactorList-class IntegerList IntegerList-class lapply,CompressedAtomicList-method LogicalList LogicalList-class NumericList NumericList-class order,List-method ranges,CompressedRleList-method ranges,RleList-method rank,List-method RawList RawList-class RleList RleList,AtomicList,RleList-method RleList-class runLength,CompressedRleList-method runLength,RleList-method runValue,CompressedRleList-method runValue,RleList-method runValue<-,CompressedRleList-method runValue<-,SimpleRleList-method show,AtomicList-method show,RleList-method SimpleAtomicList SimpleAtomicList-class SimpleCharacterList SimpleCharacterList-class SimpleComplexList SimpleComplexList-class SimpleFactorList SimpleFactorList-class SimpleIntegerList SimpleIntegerList-class SimpleLogicalList SimpleLogicalList-class SimpleNumericList SimpleNumericList-class SimpleRawList SimpleRawList-class SimpleRleList SimpleRleList-class sort,List-method table,AtomicList-method table,SimpleAtomicList-method unique,CompressedList-method unique,RleList-method unlist,SimpleFactorList-method unlist,SimpleRleList-method
Common operations on AtomicList objects	all,CompressedAtomicList-method all,CompressedRleList-method any,CompressedAtomicList-method anyNA,CompressedAtomicList-method AtomicList-utils chartr,ANY,ANY,CompressedCharacterList-method chartr,ANY,ANY,CompressedRleList-method chartr,ANY,ANY,SimpleCharacterList-method chartr,ANY,ANY,SimpleRleList-method Complex,AtomicList-method Complex,CompressedAtomicList-method cor,AtomicList,AtomicList-method cov,AtomicList,AtomicList-method cummax,CompressedAtomicList-method cummin,CompressedAtomicList-method cumprod,CompressedAtomicList-method cumsum,CompressedAtomicList-method diff,CompressedAtomicList-method diff.AtomicList endsWith,CharacterList,ANY-method endsWith,RleList,ANY-method gsub,ANY,ANY,CompressedCharacterList-method gsub,ANY,ANY,CompressedRleList-method gsub,ANY,ANY,SimpleCharacterList-method gsub,ANY,ANY,SimpleRleList-method ifelse2 ifelse2,ANY,ANY,List-method ifelse2,ANY,List,ANY-method ifelse2,CompressedLogicalList,ANY,ANY-method ifelse2,CompressedLogicalList,ANY,List-method ifelse2,CompressedLogicalList,List,ANY-method ifelse2,CompressedLogicalList,List,List-method ifelse2,List,ANY,ANY-method ifelse2,SimpleLogicalList,ANY,ANY-method ifelse2,SimpleLogicalList,ANY,List-method ifelse2,SimpleLogicalList,List,ANY-method ifelse2,SimpleLogicalList,List,List-method intersect,CompressedAtomicList,CompressedAtomicList-method IQR,AtomicList-method mad,AtomicList-method Math,AtomicList-method Math,CompressedAtomicList-method Math2,AtomicList-method Math2,CompressedAtomicList-method mean,AtomicList-method mean,CompressedIntegerList-method mean,CompressedLogicalList-method mean,CompressedNumericList-method mean,CompressedRleList-method median,AtomicList-method median,CompressedAtomicList-method nchar,CompressedCharacterList-method nchar,CompressedRleList-method nchar,SimpleCharacterList-method nchar,SimpleRleList-method Ops,atomic,AtomicList-method Ops,atomic,CompressedAtomicList-method Ops,AtomicList,atomic-method Ops,AtomicList,AtomicList-method Ops,AtomicList,missing-method Ops,CompressedAtomicList,atomic-method Ops,CompressedAtomicList,CompressedAtomicList-method Ops,CompressedAtomicList,SimpleAtomicList-method Ops,SimpleAtomicList,CompressedAtomicList-method order,CompressedAtomicList-method paste,CompressedAtomicList-method pmax,IntegerList-method pmax,NumericList-method pmax,RleList-method pmax.int,IntegerList-method pmax.int,NumericList-method pmax.int,RleList-method pmin,IntegerList-method pmin,NumericList-method pmin,RleList-method pmin.int,IntegerList-method pmin.int,NumericList-method pmin.int,RleList-method quantile,AtomicList-method range,CompressedIntegerList-method range,CompressedLogicalList-method range,CompressedNumericList-method rank,CompressedAtomicList-method runmean,RleList-method runmed,CompressedIntegerList-method runmed,NumericList-method runmed,RleList-method runmed,SimpleIntegerList-method runq,RleList-method runsum,RleList-method runwtsum,RleList-method sd,AtomicList-method selfmatch,CompressedAtomicList-method smoothEnds,CompressedIntegerList-method smoothEnds,NumericList-method smoothEnds,RleList-method smoothEnds,SimpleIntegerList-method startsWith,CharacterList,ANY-method startsWith,RleList,ANY-method sub,ANY,ANY,CompressedCharacterList-method sub,ANY,ANY,CompressedRleList-method sub,ANY,ANY,SimpleCharacterList-method sub,ANY,ANY,SimpleRleList-method sum,CompressedIntegerList-method sum,CompressedLogicalList-method sum,CompressedNumericList-method Summary,AtomicList-method Summary,CompressedRleList-method tolower,CompressedCharacterList-method tolower,CompressedRleList-method tolower,SimpleCharacterList-method tolower,SimpleRleList-method toupper,CompressedCharacterList-method toupper,CompressedRleList-method toupper,SimpleCharacterList-method toupper,SimpleRleList-method unstrsplit,CharacterList-method unstrsplit,RleList-method var,AtomicList,AtomicList-method var,AtomicList,missing-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
CompressedHitsList objects	as.matrix,CompressedHitsList-method class:CompressedHitsList CompressedHitsList CompressedHitsList-class from,CompressedHitsList-method nLnode,CompressedHitsList-method nRnode,CompressedHitsList-method space,CompressedHitsList-method to,CompressedHitsList-method
CompressedList objects	!,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
Coverage of a set of ranges	coverage coverage,IntegerRanges-method coverage,IntegerRangesList-method coverage,StitchedIPos-method coverage,Views-method coverage-methods
List of DataFrames	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
Group elements of a vector-like object into a list-like object	extractList extractList,ANY,ANY-method extractList,ANY-method regroup relist relist,ANY,List-method relist,ANY,PartitioningByEnd-method relist,Vector,list-method
Extract list fragments from a list-like object	equisplit extractListFragments INCOMPATIBLE_ARANGES_MSG
Finding overlapping ranges	%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
Grouping objects	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
Examples of basic manipulation of Hits objects	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
IntegerRanges objects	class:IntegerRanges IntegerRanges IntegerRanges-class
IntegerRangesList objects	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
Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object	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
Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object	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
IPos objects	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
IPosRanges objects	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<-
Comparing and ordering ranges	IPosRanges-comparison is.unsorted,IPosRanges-method match,IPosRanges,IPosRanges-method order,IPosRanges-method pcompare pcompare,IPosRanges,IPosRanges-method rangeComparisonCodeToLetter selfmatch,IPosRanges-method
IRanges and NormalIRanges objects	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
The IRanges constructor and supporting functions	IRanges IRanges-constructor solveUserSEW
IRanges utility functions	asNormalIRanges breakInChunks coerce,IRanges,NormalIRanges-method IRanges-utils successiveIRanges whichAsIRanges
List of IRanges and NormalIRanges	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
MaskCollection objects	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
Split elements belonging to multiple groups	multisplit
Nested Containment List objects	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
Finding the nearest range/position neighbor	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
Squeeze the ranges out of a range-based object	range-squeezers ranges rglist rglist,Pairs-method
Selection of ranges and columns	coerce,IntegerRangesList,RangedSelection-method colnames,RangedSelection-method colnames<-,RangedSelection-method RangedSelection RangedSelection-class ranges,RangedSelection-method ranges<-,RangedSelection-method
Read a mask from a file	read.agpMask read.gapMask read.liftMask read.Mask read.rmMask read.trfMask
reverse	reverse reverse,character-method reverse,IRanges-method reverse,MaskCollection-method reverse,NormalIRanges-method reverse,Views-method
Rle objects (old man page)	coerce,Rle,IRanges-method coerce,Rle,NormalIRanges-method findRange findRange,Rle-method ranges,Rle-method splitRanges splitRanges,Rle-method splitRanges,vector_OR_factor-method
The RleViews class	class:RleViews RleViews RleViews-class show,RleViews-method Views,Rle-method
List of RleViews	coerce,RleViewsList,IRangesList-method coerce,RleViewsList,SimpleIRangesList-method RleViewsList RleViewsList-class SimpleRleViewsList-class subject,SimpleRleViewsList-method Views,RleList-method
2 methods that should be documented somewhere else	split<-,Vector-method unsplit,List-method
Set operations on IntegerRanges and IntegerRangesList objects	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 pintersect,Pairs,missing-method psetdiff psetdiff,IntegerRanges,IntegerRanges-method psetdiff,Pairs,missing-method punion punion,IntegerRanges,IntegerRanges-method punion,Pairs,missing-method setdiff setdiff,CompressedIRangesList,CompressedIRangesList-method setdiff,IntegerRanges,IntegerRanges-method setdiff,IntegerRangesList,IntegerRangesList-method setdiff,Pairs,missing-method setops-methods union union,CompressedIRangesList,CompressedIRangesList-method union,IntegerRanges,IntegerRanges-method union,IntegerRangesList,IntegerRangesList-method union,Pairs,missing-method
Slice a vector-like or list-like object	slice slice,ANY-method slice,Rle-method slice,RleList-method slice-methods
Vector objects (old man page)	eval eval,expression,Vector-method eval,language,Vector-method tapply,ANY,Vector-method tapply,Vector,ANY-method tapply,Vector,Vector-method window<-,factor-method window<-,Vector-method window<-,vector-method window<-.factor window<-.Vector window<-.vector with,Vector-method
Summarize views on a vector-like object with numeric values	max,Views-method mean,Views-method min,Views-method sum,Views-method Summary,Views-method view-summarization-methods viewApply viewApply,RleViews-method viewApply,RleViewsList-method viewApply,Views-method viewMaxs viewMaxs,RleViews-method viewMaxs,RleViewsList-method viewMeans viewMeans,RleViews-method viewMeans,RleViewsList-method viewMins viewMins,RleViews-method viewMins,RleViewsList-method viewRangeMaxs viewRangeMaxs,RleViews-method viewRangeMaxs,RleViewsList-method viewRangeMins viewRangeMins,RleViews-method viewRangeMins,RleViewsList-method viewSums viewSums,RleViews-method viewSums,RleViewsList-method viewWhichMaxs viewWhichMaxs,RleViews-method viewWhichMaxs,RleViewsList-method viewWhichMins viewWhichMins,RleViews-method viewWhichMins,RleViewsList-method which.max,Views-method which.min,Views-method
Views objects	as.matrix,Views-method bindROWS,Views-method class:Views coerce,Vector,Views-method coerce,Views,IntegerRanges-method coerce,Views,IRanges-method coerce,Views,NormalIRanges-method end<-,Views-method names,Views-method names<-,Views-method parallel_slot_names,Views-method ranges,Views-method ranges<- ranges<-,Views-method start,Views-method start<-,Views-method subject subject,Views-method subviews subviews,Views-method successiveViews trim trim,Views-method unlist,Views-method Views Views-class width,Views-method width<-,Views-method
List of Views	as.matrix,ViewsList-method class:SimpleViewsList class:ViewsList end,SimpleViewsList-method ranges,SimpleViewsList-method SimpleViewsList SimpleViewsList-class start,SimpleViewsList-method ViewsList ViewsList-class width,SimpleViewsList-method