!,CompressedLogicalList-method	AtomicList-class
!,CompressedRleList-method	AtomicList-class
!,Rle-method	Rle-class
!,SimpleLogicalList-method	AtomicList-class
!,SimpleRleList-method	AtomicList-class
!=,ANY,Vector-method	Vector-comparison
!=,Vector,ANY-method	Vector-comparison
!=,Vector,Vector-method	Vector-comparison
$,List-method	List-class
$<-,CompressedList-method	SimpleList-class
$<-,List-method	List-class
$<-,RangedData-method	RangedData-class
$<-,SimpleList-method	SimpleList-class
%in%,ANY,Vector-method	Vector-comparison
%in%,CompressedAtomicList,atomic-method	AtomicList-class
%in%,CompressedAtomicList,AtomicList-method	AtomicList-class
%in%,CompressedRleList,atomic-method	AtomicList-class
%in%,CompressedRleList,AtomicList-method	AtomicList-class
%in%,RangedData,RangedData-method	findOverlaps-methods
%in%,RangedData,RangesList-method	findOverlaps-methods
%in%,Ranges,Ranges-method	Ranges-comparison
%in%,RangesList,RangedData-method	findOverlaps-methods
%in%,RangesList,RangesList-method	findOverlaps-methods
%in%,Rle,ANY-method	Rle-class
%in%,SimpleAtomicList,atomic-method	AtomicList-class
%in%,SimpleAtomicList,AtomicList-method	AtomicList-class
%in%,SimpleRleList,atomic-method	AtomicList-class
%in%,SimpleRleList,AtomicList-method	AtomicList-class
%in%,Vector,ANY-method	Vector-comparison
%in%,Vector,Vector-method	Vector-comparison
%in%,Vector,Views-method	findOverlaps-methods
%in%,Vector,ViewsList-method	findOverlaps-methods
%in%,Views,Vector-method	findOverlaps-methods
%in%,Views,Views-method	findOverlaps-methods
%in%,ViewsList,Vector-method	findOverlaps-methods
%in%,ViewsList,ViewsList-method	findOverlaps-methods
%outside%	findOverlaps-methods
%over%	findOverlaps-methods
%within%	findOverlaps-methods
.Call2	IRanges-internals
<,ANY,Vector-method	Vector-comparison
<,Vector,ANY-method	Vector-comparison
<,Vector,Vector-method	Vector-comparison
<=,ANY,Vector-method	Vector-comparison
<=,Vector,ANY-method	Vector-comparison
<=,Vector,Vector-method	Vector-comparison
==,ANY,Vector-method	Vector-comparison
==,Vector,ANY-method	Vector-comparison
==,Vector,Vector-method	Vector-comparison
>,ANY,Vector-method	Vector-comparison
>,Vector,ANY-method	Vector-comparison
>,Vector,Vector-method	Vector-comparison
>=,ANY,Vector-method	Vector-comparison
>=,Vector,ANY-method	Vector-comparison
>=,Vector,Vector-method	Vector-comparison
active	MaskCollection-class
active,FilterRules-method	FilterRules-class
active,MaskCollection-method	MaskCollection-class
active<-	MaskCollection-class
active<-,FilterRules-method	FilterRules-class
active<-,MaskCollection-method	MaskCollection-class
aggregate,CompressedList-method	SimpleList-class
aggregate,data.frame-method	Vector-class
aggregate,DataTable-method	DataTable-API
aggregate,formula-method	DataFrame-class
aggregate,matrix-method	Vector-class
aggregate,Rle-method	Rle-class
aggregate,SimpleList-method	SimpleList-class
aggregate,ts-method	Vector-class
aggregate,Vector-method	Vector-class
aggregate,vector-method	Vector-class
aggregate.Rle	Rle-class
all,CompressedRleList-method	AtomicList-class
Annotated	Annotated-class
Annotated-class	Annotated-class
append,FilterRules,FilterRules-method	FilterRules-class
append,MaskCollection,MaskCollection-method	MaskCollection-class
append,Vector,Vector-method	Vector-class
applyFun	RDApplyParams-class
applyFun,RDApplyParams-method	RDApplyParams-class
applyFun<-	RDApplyParams-class
applyFun<-,RDApplyParams-method	RDApplyParams-class
applyParams	RDApplyParams-class
applyParams,RDApplyParams-method	RDApplyParams-class
applyParams<-	RDApplyParams-class
applyParams<-,RDApplyParams-method	RDApplyParams-class
as.character,Rle-method	Rle-class
as.character,Vector-method	Vector-class
as.complex,Rle-method	Rle-class
as.complex,Vector-method	Vector-class
as.data.frame,DataFrame-method	DataFrame-class
as.data.frame,DataFrameList-method	DataFrameList-class
as.data.frame,GappedRanges-method	GappedRanges-class
as.data.frame,Hits-method	Hits-class
as.data.frame,OverlapEncodings-method	OverlapEncodings-class
as.data.frame,RangedData-method	RangedData-class
as.data.frame,Ranges-method	Ranges-class
as.data.frame,RangesList-method	RangesList-class
as.data.frame,Rle-method	Rle-class
as.data.frame,Vector-method	Vector-class
as.data.frame.DataFrame	DataFrame-class
as.data.frame.DataFrameList	DataFrameList-class
as.data.frame.GappedRanges	GappedRanges-class
as.data.frame.Hits	Hits-class
as.data.frame.OverlapEncodings	OverlapEncodings-class
as.data.frame.RangedData	RangedData-class
as.data.frame.Ranges	Ranges-class
as.data.frame.RangesList	RangesList-class
as.data.frame.Rle	Rle-class
as.data.frame.Vector	Vector-class
as.double,Vector-method	Vector-class
as.env	List-class
as.env,DataTable-method	DataTable-API
as.env,List-method	List-class
as.env,RangedData-method	RangedData-class
as.factor,Rle-method	Rle-class
as.integer,Ranges-method	Ranges-class
as.integer,Rle-method	Rle-class
as.integer,Vector-method	Vector-class
as.list,CompressedAtomicList-method	AtomicList-class
as.list,CompressedList-method	SimpleList-class
as.list,CompressedNormalIRangesList-method	IRangesList-class
as.list,Hits-method	Hits-class
as.list,List-method	List-class
as.list,Rle-method	Rle-class
as.list,SimpleList-method	SimpleList-class
as.list.CompressedList	SimpleList-class
as.list.CompressedNormalIRangesList	IRangesList-class
as.list.Hits	Hits-class
as.list.List	List-class
as.list.Rle	Rle-class
as.list.SimpleList	SimpleList-class
as.logical,Rle-method	Rle-class
as.logical,Vector-method	Vector-class
as.matrix,CompressedHitsList-method	HitsList-class
as.matrix,DataFrame-method	DataFrame-class
as.matrix,Hits-method	Hits-class
as.matrix,HitsList-method	HitsList-class
as.matrix,Ranges-method	Ranges-class
as.matrix,Views-method	Views-class
as.matrix,ViewsList-method	ViewsList-class
as.numeric,Rle-method	Rle-class
as.numeric,Vector-method	Vector-class
as.raw,Rle-method	Rle-class
as.raw,Vector-method	Vector-class
as.table,Hits-method	Hits-class
as.table,HitsList-method	HitsList-class
as.vector,AtomicList-method	AtomicList-class
as.vector,Rle-method	Rle-class
as.vectorORfactor	Rle-class
as.vectorORfactor,Rle-method	Rle-class
asNormalIRanges	IRanges-utils
AtomicList	AtomicList-class
AtomicList-class	AtomicList-class
breakInChunks	IRanges-utils
by,DataTable-method	DataTable-API
c,CompressedList-method	SimpleList-class
c,FilterRules-method	FilterRules-class
c,GappedRanges-method	GappedRanges-class
c,IRanges-method	IRanges-class
c,RangedData-method	RangedData-class
c,Rle-method	Rle-class
c,SimpleList-method	SimpleList-class
c,Vector-method	Vector-class
c,Views-method	Views-class
cbind,DataFrame-method	DataFrame-class
cbind,DataFrameList-method	DataFrameList-class
cbind,DataTable-method	DataTable-API
cbind,FilterMatrix-method	FilterMatrix-class
CharacterList	AtomicList-class
CharacterList-class	AtomicList-class
characterORNULL	IRanges-internals
characterORNULL-class	IRanges-internals
chartr,ANY,ANY,CompressedCharacterList-method	AtomicList-class
chartr,ANY,ANY,CompressedRleList-method	AtomicList-class
chartr,ANY,ANY,Rle-method	Rle-class
chartr,ANY,ANY,SimpleCharacterList-method	AtomicList-class
chartr,ANY,ANY,SimpleRleList-method	AtomicList-class
class:AtomicList	AtomicList-class
class:CharacterList	AtomicList-class
class:characterORNULL	IRanges-internals
class:ComplexList	AtomicList-class
class:CompressedAtomicList	AtomicList-class
class:CompressedCharacterList	AtomicList-class
class:CompressedComplexList	AtomicList-class
class:CompressedIntegerList	AtomicList-class
class:CompressedIRangesList	IRangesList-class
class:CompressedLogicalList	AtomicList-class
class:CompressedNormalIRangesList	IRangesList-class
class:CompressedNumericList	AtomicList-class
class:CompressedRawList	AtomicList-class
class:CompressedRleList	AtomicList-class
class:DataFrame	DataFrame-class
class:DataTable	DataTable-API
class:DataTableORNULL	DataTable-API
class:Dups	Grouping-class
class:functionORNULL	IRanges-internals
class:GappedRanges	GappedRanges-class
class:Grouping	Grouping-class
class:H2LGrouping	Grouping-class
class:IntegerList	AtomicList-class
class:IRanges	IRanges-class
class:IRangesList	IRangesList-class
class:List	List-class
class:LogicalList	AtomicList-class
class:MaskCollection	MaskCollection-class
class:NormalIRanges	IRanges-class
class:NormalIRangesList	IRangesList-class
class:NumericList	AtomicList-class
class:OverlapEncodings	OverlapEncodings-class
class:Partitioning	Grouping-class
class:PartitioningByEnd	Grouping-class
class:PartitioningByWidth	Grouping-class
class:RangedData	RangedData-class
class:Ranges	Ranges-class
class:RangesList-class	RangesList-class
class:RangesORmissing	nearest-methods
class:RawList	AtomicList-class
class:Rle	Rle-class
class:RleList	AtomicList-class
class:RleViews	RleViews-class
class:SimpleAtomicList	AtomicList-class
class:SimpleCharacterList	AtomicList-class
class:SimpleComplexList	AtomicList-class
class:SimpleIntegerList	AtomicList-class
class:SimpleIRangesList	IRangesList-class
class:SimpleLogicalList	AtomicList-class
class:SimpleNormalIRangesList	IRangesList-class
class:SimpleNumericList	AtomicList-class
class:SimpleRangesList-class	RangesList-class
class:SimpleRawList	AtomicList-class
class:SimpleRleList	AtomicList-class
class:SimpleViewsList	ViewsList-class
class:Vector	Vector-class
class:Views	Views-class
class:ViewsList	ViewsList-class
classNameForDisplay	classNameForDisplay-methods
classNameForDisplay,ANY-method	classNameForDisplay-methods
classNameForDisplay,AsIs-method	classNameForDisplay-methods
classNameForDisplay,CompressedList-method	classNameForDisplay-methods
classNameForDisplay,CompressedNormalIRangesList-method	classNameForDisplay-methods
classNameForDisplay,SimpleList-method	classNameForDisplay-methods
classNameForDisplay,SimpleNormalIRangesList-method	classNameForDisplay-methods
coerce,ANY,AsIs-method	DataFrame-class
coerce,ANY,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,ANY,DataFrame-method	DataFrame-class
coerce,ANY,List-method	List-class
coerce,ANY,SimpleList-method	SimpleList-class
coerce,ANY,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,ANY,vector-method	IRanges-internals
coerce,AsIs,DataFrame-method	DataFrame-class
coerce,AtomicList,CharacterList-method	AtomicList-class
coerce,AtomicList,ComplexList-method	AtomicList-class
coerce,AtomicList,IntegerList-method	AtomicList-class
coerce,AtomicList,LogicalList-method	AtomicList-class
coerce,AtomicList,NumericList-method	AtomicList-class
coerce,AtomicList,RawList-method	AtomicList-class
coerce,AtomicList,RleList-method	AtomicList-class
coerce,AtomicList,RleViews-method	RleViews-class
coerce,character,Rle-method	Rle-class
coerce,complex,Rle-method	Rle-class
coerce,CompressedAtomicList,list-method	AtomicList-class
coerce,CompressedIRangesList,CompressedNormalIRangesList-method	IRangesList-class
coerce,CompressedIRangesList,GappedRanges-method	GappedRanges-class
coerce,CompressedIRangesList,IntervalForest-method	IntervalForest-class
coerce,CompressedNormalIRangesList,GappedRanges-method	GappedRanges-class
coerce,CompressedRleList,CompressedIRangesList-method	AtomicList-class
coerce,data.frame,DataFrame-method	DataFrame-class
coerce,data.frame,RangedData-method	RangedData-class
coerce,DataFrame,data.frame-method	DataFrame-class
coerce,DataFrameList,DataFrame-method	DataFrameList-class
coerce,DataTable,RangedData-method	RangedData-class
coerce,factor,Rle-method	Rle-class
coerce,GappedRanges,CompressedIRangesList-method	GappedRanges-class
coerce,GappedRanges,CompressedNormalIRangesList-method	GappedRanges-class
coerce,GappedRanges,IRangesList-method	GappedRanges-class
coerce,GappedRanges,NormalIRangesList-method	GappedRanges-class
coerce,GappedRanges,RangesList-method	GappedRanges-class
coerce,Hits,DataFrame-method	Hits-class
coerce,Hits,List-method	Hits-class
coerce,Hits,list-method	Hits-class
coerce,integer,DataFrame-method	DataFrame-class
coerce,integer,IRanges-method	IRanges-class
coerce,integer,List-method	List-class
coerce,integer,NormalIRanges-method	IRanges-class
coerce,integer,Rle-method	Rle-class
coerce,IntervalForest,CompressedIRangesList-method	IntervalForest-class
coerce,IntervalForest,IRanges-method	IntervalForest-class
coerce,IntervalTree,IRanges-method	IntervalTree-class
coerce,IRanges,IntervalTree-method	IntervalTree-class
coerce,IRanges,NormalIRanges-method	IRanges-utils
coerce,List,CompressedSplitDataFrameList-method	DataFrameList-class
coerce,list,DataFrame-method	DataFrame-class
coerce,List,list-method	List-class
coerce,List,SimpleSplitDataFrameList-method	DataFrameList-class
coerce,logical,IRanges-method	IRanges-class
coerce,logical,NormalIRanges-method	IRanges-class
coerce,logical,Rle-method	Rle-class
coerce,LogicalList,CompressedIRangesList-method	RangesList-class
coerce,LogicalList,CompressedNormalIRangesList-method	RangesList-class
coerce,LogicalList,IRangesList-method	RangesList-class
coerce,LogicalList,NormalIRangesList-method	RangesList-class
coerce,LogicalList,SimpleIRangesList-method	RangesList-class
coerce,LogicalList,SimpleNormalIRangesList-method	RangesList-class
coerce,MaskCollection,NormalIRanges-method	MaskCollection-class
coerce,matrix,DataFrame-method	DataFrame-class
coerce,NULL,DataFrame-method	DataFrame-class
coerce,numeric,IRanges-method	IRanges-class
coerce,numeric,NormalIRanges-method	IRanges-class
coerce,numeric,Rle-method	Rle-class
coerce,RangedData,CompressedIRangesList-method	RangedData-class
coerce,RangedData,DataFrame-method	RangedData-class
coerce,RangedData,IRangesList-method	RangedData-class
coerce,RangedData,RangesList-method	RangedData-class
coerce,Ranges,IntervalTree-method	IntervalTree-class
coerce,Ranges,IRanges-method	IRanges-class
coerce,Ranges,PartitioningByEnd-method	Grouping-class
coerce,Ranges,PartitioningByWidth-method	Grouping-class
coerce,Ranges,RangedData-method	RangedData-class
coerce,RangesList,CompressedIRangesList-method	RangesList-class
coerce,RangesList,CompressedNormalIRangesList-method	RangesList-class
coerce,RangesList,IntervalForest-method	IntervalForest-class
coerce,RangesList,IRangesList-method	RangesList-class
coerce,RangesList,NormalIRangesList-method	RangesList-class
coerce,RangesList,RangedData-method	RangedData-class
coerce,RangesList,RangedSelection-method	RangedSelection-class
coerce,RangesList,SimpleIRangesList-method	RangesList-class
coerce,RangesList,SimpleNormalIRangesList-method	RangesList-class
coerce,RangesList,SimpleRangesList-method	RangesList-class
coerce,RangesMapping,RangedData-method	RangesMapping-class
coerce,raw,Rle-method	Rle-class
coerce,Rle,character-method	Rle-class
coerce,Rle,complex-method	Rle-class
coerce,Rle,data.frame-method	Rle-class
coerce,Rle,factor-method	Rle-class
coerce,Rle,integer-method	Rle-class
coerce,Rle,IRanges-method	Rle-class
coerce,Rle,list-method	Rle-class
coerce,Rle,logical-method	Rle-class
coerce,Rle,NormalIRanges-method	Rle-class
coerce,Rle,numeric-method	Rle-class
coerce,Rle,RangedData-method	RangedData-class
coerce,Rle,raw-method	Rle-class
coerce,Rle,vector-method	Rle-class
coerce,RleList,CompressedIRangesList-method	RangesList-class
coerce,RleList,CompressedNormalIRangesList-method	RangesList-class
coerce,RleList,IRangesList-method	RangesList-class
coerce,RleList,NormalIRangesList-method	RangesList-class
coerce,RleList,RangedData-method	RangedData-class
coerce,RleList,SimpleIRangesList-method	RangesList-class
coerce,RleList,SimpleNormalIRangesList-method	RangesList-class
coerce,RleViewsList,CompressedIRangesList-method	RleViewsList-class
coerce,RleViewsList,IRangesList-method	RleViewsList-class
coerce,RleViewsList,RangedData-method	RangedData-class
coerce,RleViewsList,SimpleIRangesList-method	RleViewsList-class
coerce,SimpleIRangesList,SimpleNormalIRangesList-method	IRangesList-class
coerce,SimpleList,DataFrame-method	DataFrame-class
coerce,SimpleRangesList,SimpleIRangesList-method	RangesList-class
coerce,SplitDataFrameList,DataFrame-method	DataFrameList-class
coerce,table,DataFrame-method	DataFrame-class
coerce,vector,AtomicList-method	AtomicList-class
coerce,Vector,character-method	Vector-class
coerce,Vector,complex-method	Vector-class
coerce,vector,CompressedCharacterList-method	AtomicList-class
coerce,vector,CompressedComplexList-method	AtomicList-class
coerce,vector,CompressedIntegerList-method	AtomicList-class
coerce,vector,CompressedLogicalList-method	AtomicList-class
coerce,vector,CompressedNumericList-method	AtomicList-class
coerce,vector,CompressedRawList-method	AtomicList-class
coerce,vector,CompressedRleList-method	AtomicList-class
coerce,Vector,data.frame-method	Vector-class
coerce,Vector,DataFrame-method	DataFrame-class
coerce,vector,DataFrame-method	DataFrame-class
coerce,Vector,double-method	Vector-class
coerce,Vector,integer-method	Vector-class
coerce,Vector,logical-method	Vector-class
coerce,Vector,numeric-method	Vector-class
coerce,Vector,raw-method	Vector-class
coerce,vector,Rle-method	Rle-class
coerce,vector,SimpleCharacterList-method	AtomicList-class
coerce,vector,SimpleComplexList-method	AtomicList-class
coerce,vector,SimpleIntegerList-method	AtomicList-class
coerce,vector,SimpleLogicalList-method	AtomicList-class
coerce,vector,SimpleNumericList-method	AtomicList-class
coerce,vector,SimpleRawList-method	AtomicList-class
coerce,vector,SimpleRleList-method	AtomicList-class
coerce,Vector,vector-method	Vector-class
coerce,Vector,Views-method	Views-class
coerce,Views,IRanges-method	Views-class
coerce,Views,NormalIRanges-method	Views-class
coerce,Views,Ranges-method	Views-class
coerce,xtabs,DataFrame-method	DataFrame-class
collapse	MaskCollection-class
collapse,MaskCollection-method	MaskCollection-class
colnames,CompressedSplitDataFrameList-method	DataFrameList-class
colnames,DataFrame-method	DataFrame-class
colnames,DataFrameList-method	DataFrameList-class
colnames,RangedData-method	RangedData-class
colnames,RangedSelection-method	RangedSelection-class
colnames,SimpleSplitDataFrameList-method	DataFrameList-class
colnames<-,CompressedSplitDataFrameList-method	DataFrameList-class
colnames<-,DataFrame-method	DataFrame-class
colnames<-,RangedData-method	RangedData-class
colnames<-,RangedSelection-method	RangedSelection-class
colnames<-,SimpleDataFrameList-method	DataFrameList-class
columnMetadata	DataFrameList-class
columnMetadata,CompressedSplitDataFrameList-method	DataFrameList-class
columnMetadata,RangedData-method	RangedData-class
columnMetadata,SimpleSplitDataFrameList-method	DataFrameList-class
columnMetadata<-	DataFrameList-class
columnMetadata<-,CompressedSplitDataFrameList-method	DataFrameList-class
columnMetadata<-,RangedData-method	RangedData-class
columnMetadata<-,SimpleSplitDataFrameList-method	DataFrameList-class
compare	Vector-comparison
compare,Ranges,Ranges-method	Ranges-comparison
complete.cases,DataTable-method	DataTable-API
Complex,CompressedAtomicList-method	AtomicList-class
Complex,Rle-method	Rle-class
Complex,SimpleAtomicList-method	AtomicList-class
ComplexList	AtomicList-class
ComplexList-class	AtomicList-class
CompressedAtomicList	AtomicList-class
CompressedAtomicList-class	AtomicList-class
CompressedCharacterList	AtomicList-class
CompressedCharacterList-class	AtomicList-class
CompressedComplexList	AtomicList-class
CompressedComplexList-class	AtomicList-class
CompressedHitsList	HitsList-class
CompressedHitsList-class	HitsList-class
CompressedIntegerList	AtomicList-class
CompressedIntegerList-class	AtomicList-class
CompressedIRangesList	IRangesList-class
CompressedIRangesList-class	IRangesList-class
CompressedList	SimpleList-class
CompressedList-class	SimpleList-class
CompressedLogicalList	AtomicList-class
CompressedLogicalList-class	AtomicList-class
CompressedNormalIRangesList	IRangesList-class
CompressedNormalIRangesList-class	IRangesList-class
CompressedNumericList	AtomicList-class
CompressedNumericList-class	AtomicList-class
CompressedRawList	AtomicList-class
CompressedRawList-class	AtomicList-class
CompressedRleList	AtomicList-class
CompressedRleList-class	AtomicList-class
CompressedSplitDataFrameList-class	DataFrameList-class
cor,AtomicList,AtomicList-method	AtomicList-class
cor,Rle,Rle-method	Rle-class
countMatches	Vector-comparison
countMatches,ANY,ANY-method	Vector-comparison
countMatches,RangedData,RangedData-method	findOverlaps-methods
countMatches,RangedData,RangesList-method	findOverlaps-methods
countMatches,Ranges,Ranges-method	Ranges-comparison
countMatches,RangesList,RangedData-method	findOverlaps-methods
countMatches,RangesList,RangesList-method	findOverlaps-methods
countMatches,Vector,Views-method	findOverlaps-methods
countMatches,Vector,ViewsList-method	findOverlaps-methods
countMatches,Views,Vector-method	findOverlaps-methods
countMatches,Views,Views-method	findOverlaps-methods
countMatches,ViewsList,Vector-method	findOverlaps-methods
countMatches,ViewsList,ViewsList-method	findOverlaps-methods
countOverlaps	findOverlaps-methods
countOverlaps,ANY,missing-method	findOverlaps-methods
countOverlaps,ANY,Vector-method	findOverlaps-methods
countOverlaps,RangedData,RangedData-method	findOverlaps-methods
countOverlaps,RangedData,RangesList-method	findOverlaps-methods
countOverlaps,RangesList,IntervalForest-method	findOverlaps-methods
countOverlaps,RangesList,RangedData-method	findOverlaps-methods
countOverlaps,RangesList,RangesList-method	findOverlaps-methods
countOverlaps,Vector,ViewsList-method	findOverlaps-methods
countOverlaps,ViewsList,Vector-method	findOverlaps-methods
countOverlaps,ViewsList,ViewsList-method	findOverlaps-methods
countQueryHits	Hits-class
countQueryHits,Hits-method	Hits-class
countSubjectHits	Hits-class
countSubjectHits,Hits-method	Hits-class
cov,AtomicList,AtomicList-method	AtomicList-class
cov,Rle,Rle-method	Rle-class
coverage	coverage-methods
coverage,RangedData-method	coverage-methods
coverage,Ranges-method	coverage-methods
coverage,RangesList-method	coverage-methods
coverage,Views-method	coverage-methods
coverage-methods	coverage-methods
cummax,CompressedAtomicList-method	AtomicList-class
cummin,CompressedAtomicList-method	AtomicList-class
cumprod,CompressedAtomicList-method	AtomicList-class
cumsum,CompressedAtomicList-method	AtomicList-class
DataFrame	DataFrame-class
DataFrame-class	DataFrame-class
DataFrameList	DataFrameList-class
DataFrameList-class	DataFrameList-class
DataTable	DataTable-API
DataTable-API	DataTable-API
DataTable-class	DataTable-API
DataTable-stats	DataTable-stats
DataTableORNULL	DataTable-API
DataTableORNULL-class	DataTable-API
desc	MaskCollection-class
desc,MaskCollection-method	MaskCollection-class
desc<-	MaskCollection-class
desc<-,MaskCollection-method	MaskCollection-class
diff,IntegerList-method	AtomicList-class
diff,NumericList-method	AtomicList-class
diff,Rle-method	Rle-class
diff,RleList-method	AtomicList-class
diff.Rle	Rle-class
dim,DataFrameList-method	DataFrameList-class
dim,DataTable-method	DataTable-API
dim,RangesMapping-method	RangesMapping-class
dimnames,DataFrameList-method	DataFrameList-class
dimnames,DataTable-method	DataTable-API
dimnames<-,DataFrameList-method	DataFrameList-class
dimnames<-,DataTable-method	DataTable-API
disjoin	inter-range-methods
disjoin,CompressedIRangesList-method	inter-range-methods
disjoin,IntervalForest-method	inter-range-methods
disjoin,Ranges-method	inter-range-methods
disjoin,RangesList-method	inter-range-methods
disjointBins	inter-range-methods
disjointBins,Ranges-method	inter-range-methods
disjointBins,RangesList-method	inter-range-methods
distance	nearest-methods
distance,Ranges,Ranges-method	nearest-methods
distanceToNearest	nearest-methods
distanceToNearest,Ranges,RangesORmissing-method	nearest-methods
drop,AtomicList-method	AtomicList-class
duplicated,AtomicList-method	AtomicList-class
duplicated,CompressedAtomicList-method	AtomicList-class
duplicated,DataTable-method	DataTable-API
duplicated,Dups-method	Grouping-class
duplicated,Ranges-method	Ranges-comparison
duplicated,Rle-method	Rle-class
duplicated,Vector-method	Vector-comparison
duplicated.AtomicList	AtomicList-class
duplicated.CompressedAtomicList	AtomicList-class
duplicated.DataTable	DataTable-API
duplicated.Dups	Grouping-class
duplicated.Ranges	Ranges-comparison
duplicated.Rle	Rle-class
duplicated.Vector	Vector-comparison
Dups	Grouping-class
Dups-class	Grouping-class
elementLengths	List-class
elementLengths,ANY-method	List-class
elementLengths,CompressedList-method	List-class
elementLengths,GappedRanges-method	GappedRanges-class
elementLengths,IntervalForest-method	IntervalForest-class
elementLengths,List-method	List-class
elementLengths,list-method	List-class
elementLengths,RangedData-method	RangedData-class
elementLengths,Ranges-method	Ranges-class
elementLengths,Views-method	Views-class
elementMetadata	Vector-class
elementMetadata,Vector-method	Vector-class
elementMetadata<-	Vector-class
elementMetadata<-,Vector-method	Vector-class
elementType	List-class
elementType,List-method	List-class
elementType,vector-method	List-class
encodeOverlaps	encodeOverlaps-methods
encodeOverlaps,Ranges,RangesList-method	encodeOverlaps-methods
encodeOverlaps,RangesList,Ranges-method	encodeOverlaps-methods
encodeOverlaps,RangesList,RangesList-method	encodeOverlaps-methods
encodeOverlaps1	encodeOverlaps-methods
encoding	OverlapEncodings-class
encoding,OverlapEncodings-method	OverlapEncodings-class
end,CompressedIRangesList-method	IRangesList-class
end,GappedRanges-method	GappedRanges-class
end,IntervalForest-method	IntervalForest-class
end,IntervalTree-method	IntervalTree-class
end,PartitioningByEnd-method	Grouping-class
end,PartitioningByWidth-method	Grouping-class
end,RangedData-method	RangedData-class
end,Ranges-method	Ranges-class
end,RangesList-method	RangesList-class
end,Rle-method	Rle-class
end,SimpleViewsList-method	ViewsList-class
end,Views-method	Views-class
end<-	Ranges-class
end<-,IRanges-method	IRanges-class
end<-,RangedData-method	RangedData-class
end<-,RangesList-method	RangesList-class
end<-,Views-method	Views-class
endoapply	endoapply
endoapply,CompressedList-method	SimpleList-class
endoapply,data.frame-method	endoapply
endoapply,List-method	List-class
endoapply,list-method	endoapply
endoapply,RangedData-method	RangedData-class
endoapply,SimpleList-method	SimpleList-class
eval	List-class
eval,expression,List-method	List-class
eval,FilterRules,ANY-method	FilterRules-class
eval,language,List-method	List-class
evalSeparately	FilterRules-class
evalSeparately,FilterRules-method	FilterRules-class
expand	expand-methods
expand,DataFrame-method	expand-methods
Filter,List-method	funprog-methods
FilterMatrix	FilterMatrix-class
FilterMatrix-class	FilterMatrix-class
FilterRules	FilterRules-class
filterRules	RDApplyParams-class
filterRules,FilterMatrix-method	FilterMatrix-class
filterRules,RDApplyParams-method	RDApplyParams-class
FilterRules-class	FilterRules-class
filterRules<-	RDApplyParams-class
filterRules<-,RDApplyParams-method	RDApplyParams-class
Find,List-method	funprog-methods
findMatches	Vector-comparison
findMatches,ANY,ANY-method	Vector-comparison
findMatches,RangedData,RangedData-method	findOverlaps-methods
findMatches,RangedData,RangesList-method	findOverlaps-methods
findMatches,Ranges,Ranges-method	Ranges-comparison
findMatches,RangesList,RangedData-method	findOverlaps-methods
findMatches,RangesList,RangesList-method	findOverlaps-methods
findMatches,Vector,Views-method	findOverlaps-methods
findMatches,Vector,ViewsList-method	findOverlaps-methods
findMatches,Views,Vector-method	findOverlaps-methods
findMatches,Views,Views-method	findOverlaps-methods
findMatches,ViewsList,Vector-method	findOverlaps-methods
findMatches,ViewsList,ViewsList-method	findOverlaps-methods
findOverlaps	findOverlaps-methods
findOverlaps,integer,Ranges-method	findOverlaps-methods
findOverlaps,RangedData,RangedData-method	findOverlaps-methods
findOverlaps,RangedData,RangesList-method	findOverlaps-methods
findOverlaps,Ranges,IntervalTree-method	findOverlaps-methods
findOverlaps,Ranges,Ranges-method	findOverlaps-methods
findOverlaps,RangesList,IntervalForest-method	findOverlaps-methods
findOverlaps,RangesList,RangedData-method	findOverlaps-methods
findOverlaps,RangesList,RangesList-method	findOverlaps-methods
findOverlaps,Vector,missing-method	findOverlaps-methods
findOverlaps,Vector,Views-method	findOverlaps-methods
findOverlaps,Vector,ViewsList-method	findOverlaps-methods
findOverlaps,Views,Vector-method	findOverlaps-methods
findOverlaps,Views,Views-method	findOverlaps-methods
findOverlaps,ViewsList,Vector-method	findOverlaps-methods
findOverlaps,ViewsList,ViewsList-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
findRange	Rle-class
findRange,Rle-method	Rle-class
findRun	Rle-class
findRun,Rle-method	Rle-class
first	Ranges-class
first,Ranges-method	Ranges-class
flank	intra-range-methods
flank,CompressedIRangesList-method	intra-range-methods
flank,IntervalForest-method	intra-range-methods
flank,Ranges-method	intra-range-methods
flank,RangesList-method	intra-range-methods
flippedQuery	OverlapEncodings-class
flippedQuery,OverlapEncodings-method	OverlapEncodings-class
fold	IRanges-internals
follow	nearest-methods
follow,Ranges,RangesORmissing-method	nearest-methods
functionORNULL	IRanges-internals
functionORNULL-class	IRanges-internals
funprog-methods	funprog-methods
GappedRanges	GappedRanges-class
GappedRanges-class	GappedRanges-class
gaps	inter-range-methods
gaps,CompressedIRangesList-method	inter-range-methods
gaps,IntervalForest-method	inter-range-methods
gaps,IRanges-method	inter-range-methods
gaps,MaskCollection-method	inter-range-methods
gaps,Ranges-method	inter-range-methods
gaps,RangesList-method	inter-range-methods
gaps,Views-method	inter-range-methods
get_showHeadLines	DataTable-API
get_showTailLines	DataTable-API
Grouping	Grouping-class
Grouping-class	Grouping-class
grouplength	Grouping-class
grouplength,Grouping-method	Grouping-class
grouplength,H2LGrouping-method	Grouping-class
grouplength,Partitioning-method	Grouping-class
grouprank	Grouping-class
grouprank,H2LGrouping-method	Grouping-class
gsub,ANY,ANY,CompressedCharacterList-method	AtomicList-class
gsub,ANY,ANY,CompressedRleList-method	AtomicList-class
gsub,ANY,ANY,Rle-method	Rle-class
gsub,ANY,ANY,SimpleCharacterList-method	AtomicList-class
gsub,ANY,ANY,SimpleRleList-method	AtomicList-class
H2LGrouping	Grouping-class
H2LGrouping-class	Grouping-class
head,Vector-method	Vector-class
head.Vector	Vector-class
high2low	Grouping-class
high2low,H2LGrouping-method	Grouping-class
high2low,Vector-method	Grouping-class
high2low,vector-method	Grouping-class
Hits	Hits-class
hits	RangesMapping-class
Hits-class	Hits-class
HitsList-class	HitsList-class
ifelse,ANY,ANY,Rle-method	Rle-class
ifelse,ANY,Rle,ANY-method	Rle-class
ifelse,ANY,Rle,Rle-method	Rle-class
IntegerList	AtomicList-class
IntegerList-class	AtomicList-class
inter-range-methods	inter-range-methods
intersect,CompressedIRangesList,CompressedIRangesList-method	setops-methods
intersect,Hits,Hits-method	setops-methods
intersect,IRanges,IRanges-method	setops-methods
intersect,RangesList,RangesList-method	setops-methods
IntervalForest	IntervalForest-class
IntervalForest-class	IntervalForest-class
IntervalTree	IntervalTree-class
IntervalTree-class	IntervalTree-class
intra-range-methods	intra-range-methods
IQR,AtomicList-method	AtomicList-class
IQR,Rle-method	Rle-class
IRanges	IRanges-constructor
IRanges-class	IRanges-class
IRanges-constructor	IRanges-constructor
IRanges-utils	IRanges-utils
IRangesList	IRangesList-class
IRangesList-class	IRangesList-class
is.na,CompressedAtomicList-method	AtomicList-class
is.na,CompressedRleList-method	AtomicList-class
is.na,DataTable-method	DataTable-API
is.na,Rle-method	Rle-class
is.na,SimpleAtomicList-method	AtomicList-class
is.na,SimpleRleList-method	AtomicList-class
is.unsorted,Rle-method	Rle-class
isConstant	isConstant
isConstant,array-method	isConstant
isConstant,integer-method	isConstant
isConstant,numeric-method	isConstant
isDisjoint	inter-range-methods
isDisjoint,Ranges-method	inter-range-methods
isDisjoint,RangesList-method	inter-range-methods
isEmpty	List-class
isEmpty,ANY-method	List-class
isEmpty,CompressedList-method	SimpleList-class
isEmpty,List-method	List-class
isEmpty,NormalIRanges-method	IRanges-class
isEmpty,Ranges-method	Ranges-class
isEmpty,SimpleList-method	SimpleList-class
isNormal	Ranges-class
isNormal,CompressedIRangesList-method	IRangesList-class
isNormal,IRanges-method	IRanges-class
isNormal,Ranges-method	Ranges-class
isNormal,RangesList-method	IRangesList-class
isNormal,SimpleIRangesList-method	IRangesList-class
isSingleInteger	IRanges-internals
isSingleNumber	IRanges-internals
isSingleNumberOrNA	IRanges-internals
isSingleString	IRanges-internals
isSingleStringOrNA	IRanges-internals
isTRUEorFALSE	IRanges-internals
iteratorFun	RDApplyParams-class
iteratorFun,RDApplyParams-method	RDApplyParams-class
iteratorFun<-	RDApplyParams-class
iteratorFun<-,RDApplyParams-method	RDApplyParams-class
lapply,CompressedAtomicList-method	AtomicList-class
lapply,CompressedList-method	SimpleList-class
lapply,List-method	List-class
lapply,RangedData-method	RangedData-class
lapply,SimpleList-method	SimpleList-class
last	Ranges-class
last,Ranges-method	Ranges-class
Lencoding	OverlapEncodings-class
Lencoding,character-method	OverlapEncodings-class
Lencoding,factor-method	OverlapEncodings-class
Lencoding,OverlapEncodings-method	OverlapEncodings-class
length,CompressedList-method	SimpleList-class
length,GappedRanges-method	GappedRanges-class
length,H2LGrouping-method	Grouping-class
length,Hits-method	Hits-class
length,IntervalForest-method	IntervalForest-class
length,IntervalTree-method	IntervalTree-class
length,MaskCollection-method	MaskCollection-class
length,OverlapEncodings-method	OverlapEncodings-class
length,PartitioningByEnd-method	Grouping-class
length,PartitioningByWidth-method	Grouping-class
length,RangedData-method	RangedData-class
length,Ranges-method	Ranges-class
length,RangesMapping-method	RangesMapping-class
length,Rle-method	Rle-class
length,SimpleList-method	SimpleList-class
length,Views-method	Views-class
length<-,H2LGrouping-method	Grouping-class
levels,OverlapEncodings-method	OverlapEncodings-class
levels,Rle-method	Rle-class
levels.Rle	Rle-class
levels<-,Rle-method	Rle-class
List	List-class
List-class	List-class
Lngap	OverlapEncodings-class
Lngap,character-method	OverlapEncodings-class
Lngap,factor-method	OverlapEncodings-class
Lngap,OverlapEncodings-method	OverlapEncodings-class
Loffset	OverlapEncodings-class
Loffset,OverlapEncodings-method	OverlapEncodings-class
LogicalList	AtomicList-class
LogicalList-class	AtomicList-class
low2high	Grouping-class
low2high,H2LGrouping-method	Grouping-class
mad,AtomicList-method	AtomicList-class
mad,Rle-method	Rle-class
mad.Rle	Rle-class
map	RangesMapping-class
Map,List-method	funprog-methods
mapply,List-method	List-class
Mask	MaskCollection-class
MaskCollection	MaskCollection-class
MaskCollection-class	MaskCollection-class
MaskCollection.show_frame	MaskCollection-class
maskedratio	MaskCollection-class
maskedratio,MaskCollection-method	MaskCollection-class
maskedwidth	MaskCollection-class
maskedwidth,MaskCollection-method	MaskCollection-class
match,CompressedAtomicList,atomic-method	AtomicList-class
match,CompressedAtomicList,AtomicList-method	AtomicList-class
match,CompressedRleList,atomic-method	AtomicList-class
match,CompressedRleList,AtomicList-method	AtomicList-class
match,Hits,Hits-method	Hits-class
match,RangedData,RangedData-method	findOverlaps-methods
match,RangedData,RangesList-method	findOverlaps-methods
match,Ranges,Ranges-method	Ranges-comparison
match,RangesList,RangedData-method	findOverlaps-methods
match,RangesList,RangesList-method	findOverlaps-methods
match,Rle,ANY-method	Rle-class
match,SimpleAtomicList,atomic-method	AtomicList-class
match,SimpleAtomicList,AtomicList-method	AtomicList-class
match,SimpleRleList,atomic-method	AtomicList-class
match,SimpleRleList,AtomicList-method	AtomicList-class
match,Vector,Views-method	findOverlaps-methods
match,Vector,ViewsList-method	findOverlaps-methods
match,Views,Vector-method	findOverlaps-methods
match,Views,Views-method	findOverlaps-methods
match,ViewsList,Vector-method	findOverlaps-methods
match,ViewsList,ViewsList-method	findOverlaps-methods
Math,CompressedAtomicList-method	AtomicList-class
Math,Rle-method	Rle-class
Math,SimpleAtomicList-method	AtomicList-class
Math2,CompressedAtomicList-method	AtomicList-class
Math2,Rle-method	Rle-class
Math2,SimpleAtomicList-method	AtomicList-class
max,CompressedNormalIRangesList-method	IRangesList-class
max,MaskCollection-method	MaskCollection-class
max,NormalIRanges-method	IRanges-class
max,SimpleNormalIRangesList-method	IRangesList-class
max,Views-method	view-summarization-methods
mcols	Vector-class
mcols,Vector-method	Vector-class
mcols<-	Vector-class
mcols<-,Vector-method	Vector-class
mean,AtomicList-method	AtomicList-class
mean,Rle-method	Rle-class
mean,Views-method	view-summarization-methods
mean.Rle	Rle-class
median,AtomicList-method	AtomicList-class
median,Rle-method	Rle-class
median.Rle	Rle-class
members	Grouping-class
members,Grouping-method	Grouping-class
members,H2LGrouping-method	Grouping-class
mendoapply	endoapply
mendoapply,CompressedList-method	SimpleList-class
mendoapply,data.frame-method	endoapply
mendoapply,List-method	List-class
mendoapply,list-method	endoapply
mendoapply,SimpleList-method	SimpleList-class
merge,data.frame,DataTable-method	DataTable-API
merge,DataTable,data.frame-method	DataTable-API
merge,DataTable,DataTable-method	DataTable-API
merge,missing,RangesList-method	RangesList-class
merge,RangesList,missing-method	RangesList-class
merge,RangesList,RangesList-method	RangesList-class
metadata	Annotated-class
metadata,Annotated-method	Annotated-class
metadata<-	Annotated-class
metadata<-,Annotated-method	Annotated-class
mid	Ranges-class
mid,Ranges-method	Ranges-class
min,CompressedNormalIRangesList-method	IRangesList-class
min,MaskCollection-method	MaskCollection-class
min,NormalIRanges-method	IRanges-class
min,SimpleNormalIRangesList-method	IRangesList-class
min,Views-method	view-summarization-methods
mseqapply	seqapply
mstack	Vector-class
mstack,DataFrame-method	DataFrame-class
mstack,Vector-method	Vector-class
mstack,vector-method	Vector-class
multisplit	multisplit
na.exclude	DataTable-API
na.exclude,DataTable-method	DataTable-API
na.omit	DataTable-API
na.omit,DataTable-method	DataTable-API
names,CompressedList-method	SimpleList-class
names,GappedRanges-method	GappedRanges-class
names,IntervalForest-method	IntervalForest-class
names,IRanges-method	IRanges-class
names,MaskCollection-method	MaskCollection-class
names,Partitioning-method	Grouping-class
names,RangedData-method	RangedData-class
names,SimpleList-method	SimpleList-class
names,Views-method	Views-class
names<-,CompressedList-method	SimpleList-class
names<-,GappedRanges-method	GappedRanges-class
names<-,IRanges-method	IRanges-class
names<-,MaskCollection-method	MaskCollection-class
names<-,Partitioning-method	Grouping-class
names<-,RangedData-method	RangedData-class
names<-,SimpleList-method	SimpleList-class
names<-,Views-method	Views-class
narrow	intra-range-methods
narrow,CompressedIRangesList-method	intra-range-methods
narrow,IntervalForest-method	intra-range-methods
narrow,MaskCollection-method	intra-range-methods
narrow,Ranges-method	intra-range-methods
narrow,RangesList-method	intra-range-methods
narrow,Views-method	intra-range-methods
nchar,CompressedCharacterList-method	AtomicList-class
nchar,CompressedRleList-method	AtomicList-class
nchar,Rle-method	Rle-class
nchar,SimpleCharacterList-method	AtomicList-class
nchar,SimpleRleList-method	AtomicList-class
ncol,CompressedSplitDataFrameList-method	DataFrameList-class
ncol,DataFrame-method	DataFrame-class
ncol,DataFrameList-method	DataFrameList-class
NCOL,DataTable-method	DataTable-API
ncol,RangedData-method	RangedData-class
ncol,SimpleSplitDataFrameList-method	DataFrameList-class
nearest	nearest-methods
nearest,Ranges,RangesORmissing-method	nearest-methods
nearest-methods	nearest-methods
new2	IRanges-internals
newViews	Views-class
ngap	GappedRanges-class
ngap,character-method	OverlapEncodings-class
ngap,factor-method	OverlapEncodings-class
ngap,GappedRanges-method	GappedRanges-class
ngap,OverlapEncodings-method	OverlapEncodings-class
nir_list	MaskCollection-class
nir_list,MaskCollection-method	MaskCollection-class
nobj	Grouping-class
nobj,H2LGrouping-method	Grouping-class
nobj,PartitioningByEnd-method	Grouping-class
nobj,PartitioningByWidth-method	Grouping-class
NormalIRanges	IRanges-class
NormalIRanges-class	IRanges-class
NormalIRangesList	IRangesList-class
NormalIRangesList-class	IRangesList-class
nrow,DataFrame-method	DataFrame-class
nrow,DataFrameList-method	DataFrameList-class
NROW,DataTable-method	DataTable-API
nrow,RangedData-method	RangedData-class
NROW,Vector-method	Vector-class
nrun	Rle-class
nrun,Rle-method	Rle-class
NumericList	AtomicList-class
NumericList-class	AtomicList-class
Ops,atomic,AtomicList-method	AtomicList-class
Ops,atomic,CompressedAtomicList-method	AtomicList-class
Ops,atomic,SimpleAtomicList-method	AtomicList-class
Ops,AtomicList,atomic-method	AtomicList-class
Ops,CompressedAtomicList,atomic-method	AtomicList-class
Ops,CompressedAtomicList,CompressedAtomicList-method	AtomicList-class
Ops,CompressedAtomicList,SimpleAtomicList-method	AtomicList-class
Ops,CompressedIRangesList,ANY-method	intra-range-methods
Ops,Ranges,ANY-method	intra-range-methods
Ops,Ranges,numeric-method	intra-range-methods
Ops,RangesList,ANY-method	intra-range-methods
Ops,Rle,Rle-method	Rle-class
Ops,Rle,vector-method	Rle-class
Ops,SimpleAtomicList,atomic-method	AtomicList-class
Ops,SimpleAtomicList,CompressedAtomicList-method	AtomicList-class
Ops,SimpleAtomicList,SimpleAtomicList-method	AtomicList-class
Ops,vector,Rle-method	Rle-class
order,Ranges-method	Ranges-comparison
order,Rle-method	Rle-class
OverlapEncodings	OverlapEncodings-class
OverlapEncodings-class	OverlapEncodings-class
overlapsAny	findOverlaps-methods
overlapsAny,RangedData,RangedData-method	findOverlaps-methods
overlapsAny,RangedData,RangesList-method	findOverlaps-methods
overlapsAny,Ranges,Ranges-method	findOverlaps-methods
overlapsAny,RangesList,IntervalForest-method	findOverlaps-methods
overlapsAny,RangesList,RangedData-method	findOverlaps-methods
overlapsAny,RangesList,RangesList-method	findOverlaps-methods
overlapsAny,Vector,Views-method	findOverlaps-methods
overlapsAny,Vector,ViewsList-method	findOverlaps-methods
overlapsAny,Views,Vector-method	findOverlaps-methods
overlapsAny,Views,Views-method	findOverlaps-methods
overlapsAny,ViewsList,Vector-method	findOverlaps-methods
overlapsAny,ViewsList,ViewsList-method	findOverlaps-methods
params	FilterRules-class
params,FilterClosure-method	FilterRules-class
Partitioning	Grouping-class
Partitioning-class	Grouping-class
PartitioningByEnd	Grouping-class
PartitioningByEnd-class	Grouping-class
PartitioningByWidth	Grouping-class
PartitioningByWidth-class	Grouping-class
paste,Rle-method	Rle-class
pgap	setops-methods
pgap,IRanges,IRanges-method	setops-methods
pintersect	setops-methods
pintersect,IRanges,IRanges-method	setops-methods
pmap	RangesMapping-class
pmax,IntegerList-method	AtomicList-class
pmax,NumericList-method	AtomicList-class
pmax,Rle-method	Rle-class
pmax,RleList-method	AtomicList-class
pmax.int,IntegerList-method	AtomicList-class
pmax.int,NumericList-method	AtomicList-class
pmax.int,Rle-method	Rle-class
pmax.int,RleList-method	AtomicList-class
pmin,IntegerList-method	AtomicList-class
pmin,NumericList-method	AtomicList-class
pmin,Rle-method	Rle-class
pmin,RleList-method	AtomicList-class
pmin.int,IntegerList-method	AtomicList-class
pmin.int,NumericList-method	AtomicList-class
pmin.int,Rle-method	Rle-class
pmin.int,RleList-method	AtomicList-class
Position,List-method	funprog-methods
precede	nearest-methods
precede,Ranges,RangesORmissing-method	nearest-methods
promoters	intra-range-methods
promoters,CompressedIRangesList-method	intra-range-methods
promoters,IntervalForest-method	intra-range-methods
promoters,Ranges-method	intra-range-methods
promoters,RangesList-method	intra-range-methods
promoters,Views-method	intra-range-methods
psetdiff	setops-methods
psetdiff,IRanges,IRanges-method	setops-methods
punion	setops-methods
punion,IRanges,IRanges-method	setops-methods
quantile,AtomicList-method	AtomicList-class
quantile,Rle-method	Rle-class
quantile.Rle	Rle-class
queryHits	Hits-class
queryHits,CompressedHitsList-method	HitsList-class
queryHits,Hits-method	Hits-class
queryHits,HitsList-method	HitsList-class
queryHits,RangesMapping-method	RangesMapping-class
queryLength	Hits-class
queryLength,CompressedHitsList-method	HitsList-class
queryLength,Hits-method	Hits-class
range,CompressedIRangesList-method	inter-range-methods
range,IntervalForest-method	inter-range-methods
range,RangedData-method	inter-range-methods
range,Ranges-method	inter-range-methods
range,RangesList-method	inter-range-methods
rangeComparisonCodeToLetter	Ranges-comparison
RangedData	RangedData-class
rangedData	RDApplyParams-class
rangedData,RDApplyParams-method	RDApplyParams-class
RangedData-class	RangedData-class
rangedData<-	RDApplyParams-class
rangedData<-,RDApplyParams-method	RDApplyParams-class
RangedDataList	RangedDataList-class
RangedDataList-class	RangedDataList-class
RangedSelection	RangedSelection-class
RangedSelection-class	RangedSelection-class
Ranges	Ranges-class
ranges	Views-class
ranges,CompressedRleList-method	AtomicList-class
ranges,Hits-method	findOverlaps-methods
ranges,HitsList-method	HitsList-class
ranges,RangedData-method	RangedData-class
ranges,RangedSelection-method	RangedSelection-class
ranges,RangesMapping-method	RangesMapping-class
ranges,Rle-method	Rle-class
ranges,RleList-method	AtomicList-class
ranges,SimpleViewsList-method	ViewsList-class
ranges,Views-method	Views-class
Ranges-class	Ranges-class
Ranges-comparison	Ranges-comparison
ranges<-	Views-class
ranges<-,RangedData-method	RangedData-class
ranges<-,RangedSelection-method	RangedSelection-class
ranges<-,Views-method	Views-class
RangesList	RangesList-class
RangesList-class	RangesList-class
RangesList_encodeOverlaps	encodeOverlaps-methods
RangesMapping-class	RangesMapping-class
RangesORmissing	nearest-methods
RangesORmissing-class	nearest-methods
rank,Ranges-method	Ranges-comparison
RawList	AtomicList-class
RawList-class	AtomicList-class
rbind,DataFrame-method	DataFrame-class
rbind,DataFrameList-method	DataFrameList-class
rbind,DataTable-method	DataTable-API
rbind,FilterMatrix-method	FilterMatrix-class
rbind,RangedData-method	RangedData-class
rdapply	RDApplyParams-class
rdapply,RDApplyParams-method	RDApplyParams-class
RDApplyParams	RDApplyParams-class
RDApplyParams-class	RDApplyParams-class
read.agpMask	read.Mask
read.gapMask	read.Mask
read.liftMask	read.Mask
read.Mask	read.Mask
read.rmMask	read.Mask
read.trfMask	read.Mask
recycleIntegerArg	IRanges-internals
recycleNumericArg	IRanges-internals
reduce	inter-range-methods
reduce,CompressedIRangesList-method	inter-range-methods
reduce,IntervalForest-method	inter-range-methods
reduce,IRanges-method	inter-range-methods
Reduce,List-method	funprog-methods
reduce,RangedData-method	inter-range-methods
reduce,Ranges-method	inter-range-methods
reduce,RangesList-method	inter-range-methods
reduce,Views-method	inter-range-methods
reducerFun	RDApplyParams-class
reducerFun,RDApplyParams-method	RDApplyParams-class
reducerFun<-	RDApplyParams-class
reducerFun<-,RDApplyParams-method	RDApplyParams-class
reducerParams	RDApplyParams-class
reducerParams,RDApplyParams-method	RDApplyParams-class
reducerParams<-	RDApplyParams-class
reducerParams<-,RDApplyParams-method	RDApplyParams-class
reflect	intra-range-methods
reflect,Ranges-method	intra-range-methods
relist,ANY,List-method	List-class
relist,ANY,PartitioningByEnd-method	Grouping-class
relist,Vector,list-method	Vector-class
remapHits	Hits-class
rename	Vector-class
rename,Vector-method	Vector-class
rename,vector-method	Vector-class
Rencoding	OverlapEncodings-class
Rencoding,character-method	OverlapEncodings-class
Rencoding,factor-method	OverlapEncodings-class
Rencoding,OverlapEncodings-method	OverlapEncodings-class
rep,Rle-method	Rle-class
rep,Vector-method	Vector-class
rep.int,Rle-method	Rle-class
rep.int,Vector-method	Vector-class
resize	intra-range-methods
resize,CompressedIRangesList-method	intra-range-methods
resize,IntervalForest-method	intra-range-methods
resize,IntervalList-method	intra-range-methods
resize,Ranges-method	intra-range-methods
resize,RangesList-method	intra-range-methods
restrict	intra-range-methods
restrict,CompressedIRangesList-method	intra-range-methods
restrict,IntervalForest-method	intra-range-methods
restrict,Ranges-method	intra-range-methods
restrict,RangesList-method	intra-range-methods
rev,Rle-method	Rle-class
rev,Vector-method	Vector-class
rev.Rle	Rle-class
revElements	List-class
revElements,CompressedList-method	SimpleList-class
revElements,List-method	List-class
reverse	reverse-methods
reverse,character-method	reverse-methods
reverse,IRanges-method	reverse-methods
reverse,MaskCollection-method	reverse-methods
reverse,NormalIRanges-method	reverse-methods
reverse,Views-method	reverse-methods
Rle	Rle-class
Rle,missing,missing-method	Rle-class
Rle,vectorORfactor,integer-method	Rle-class
Rle,vectorORfactor,missing-method	Rle-class
Rle,vectorORfactor,numeric-method	Rle-class
Rle-class	Rle-class
RleList	AtomicList-class
RleList,AtomicList,RleList-method	AtomicList-class
RleList-class	AtomicList-class
RleViews	RleViews-class
RleViews-class	RleViews-class
RleViewsList	RleViewsList-class
RleViewsList-class	RleViewsList-class
Rngap	OverlapEncodings-class
Rngap,character-method	OverlapEncodings-class
Rngap,factor-method	OverlapEncodings-class
Rngap,OverlapEncodings-method	OverlapEncodings-class
Roffset	OverlapEncodings-class
Roffset,OverlapEncodings-method	OverlapEncodings-class
rownames,DataFrame-method	DataFrame-class
rownames,DataFrameList-method	DataFrameList-class
rownames,RangedData-method	RangedData-class
rownames<-,CompressedSplitDataFrameList-method	DataFrameList-class
rownames<-,DataFrame-method	DataFrame-class
rownames<-,RangedData-method	RangedData-class
rownames<-,SimpleDataFrameList-method	DataFrameList-class
runLength	Rle-class
runLength,CompressedRleList-method	AtomicList-class
runLength,Rle-method	Rle-class
runLength,RleList-method	AtomicList-class
runLength<-	Rle-class
runLength<-,Rle-method	Rle-class
runmean	runstat
runmean,Rle-method	Rle-class
runmean,RleList-method	AtomicList-class
runmed,CompressedIntegerList-method	AtomicList-class
runmed,NumericList-method	AtomicList-class
runmed,Rle-method	Rle-class
runmed,RleList-method	AtomicList-class
runmed,SimpleIntegerList-method	AtomicList-class
runq	runstat
runq,Rle-method	Rle-class
runq,RleList-method	AtomicList-class
runstat	runstat
runsum	runstat
runsum,Rle-method	Rle-class
runsum,RleList-method	AtomicList-class
runValue	Rle-class
runValue,CompressedRleList-method	AtomicList-class
runValue,Rle-method	Rle-class
runValue,RleList-method	AtomicList-class
runValue<-	Rle-class
runValue<-,Rle-method	Rle-class
runwtsum	runstat
runwtsum,Rle-method	Rle-class
runwtsum,RleList-method	AtomicList-class
safeExplode	strutils
sapply,List-method	List-class
score	score
score,RangedData-method	RangedData-class
score<-	score
score<-,RangedData-method	RangedData-class
sd,AtomicList-method	AtomicList-class
sd,Rle-method	Rle-class
selfmatch	Vector-comparison
selfmatch,ANY-method	Vector-comparison
selfmatch,Ranges-method	Ranges-comparison
seqapply	seqapply
seqby	seqapply
seqselect	Vector-class
seqselect,ANY-method	Vector-class
seqselect<-	Vector-class
seqselect<-,ANY-method	Vector-class
seqsplit	seqapply
setdiff,CompressedIRangesList,CompressedIRangesList-method	setops-methods
setdiff,Hits,Hits-method	setops-methods
setdiff,IRanges,IRanges-method	setops-methods
setdiff,RangesList,RangesList-method	setops-methods
setMethods	IRanges-internals
setops-methods	setops-methods
setValidity2	IRanges-internals
shift	intra-range-methods
shift,CompressedIRangesList-method	intra-range-methods
shift,IntervalForest-method	intra-range-methods
shift,Ranges-method	intra-range-methods
shift,RangesList-method	intra-range-methods
shift,Views-method	intra-range-methods
shiftApply	Vector-class
shiftApply,Rle,Rle-method	Rle-class
shiftApply,Vector,Vector-method	Vector-class
shiftApply,vector,vector-method	Vector-class
show,AtomicList-method	AtomicList-class
show,DataTable-method	DataTable-API
show,Dups-method	Grouping-class
show,FilterClosure-method	FilterRules-class
show,FilterMatrix-method	FilterMatrix-class
show,GappedRanges-method	GappedRanges-class
show,Grouping-method	Grouping-class
show,Hits-method	Hits-class
show,IntervalForest-method	IntervalForest-class
show,List-method	List-class
show,MaskCollection-method	MaskCollection-class
show,OverlapEncodings-method	OverlapEncodings-class
show,RangedData-method	RangedData-class
show,Ranges-method	Ranges-class
show,RangesList-method	RangesList-class
show,Rle-method	Rle-class
show,RleList-method	AtomicList-class
show,RleViews-method	RleViews-class
show,SplitDataFrameList-method	DataFrameList-class
showAsCell	Vector-class
showAsCell,ANY-method	Vector-class
showAsCell,AtomicList-method	AtomicList-class
showAsCell,list-method	Vector-class
showAsCell,Ranges-method	Ranges-class
showAsCell,RangesList-method	RangesList-class
showAsCell,Rle-method	Rle-class
showAsCell,Vector-method	Vector-class
SimpleAtomicList	AtomicList-class
SimpleAtomicList-class	AtomicList-class
SimpleCharacterList	AtomicList-class
SimpleCharacterList-class	AtomicList-class
SimpleComplexList	AtomicList-class
SimpleComplexList-class	AtomicList-class
SimpleDataFrameList-class	DataFrameList-class
SimpleIntegerList	AtomicList-class
SimpleIntegerList-class	AtomicList-class
SimpleIRangesList	IRangesList-class
SimpleIRangesList-class	IRangesList-class
SimpleList	SimpleList-class
SimpleList-class	SimpleList-class
SimpleLogicalList	AtomicList-class
SimpleLogicalList-class	AtomicList-class
SimpleNormalIRangesList	IRangesList-class
SimpleNormalIRangesList-class	IRangesList-class
SimpleNumericList	AtomicList-class
SimpleNumericList-class	AtomicList-class
SimpleRangesList	RangesList-class
SimpleRangesList-class	RangesList-class
SimpleRawList	AtomicList-class
SimpleRawList-class	AtomicList-class
SimpleRleList	AtomicList-class
SimpleRleList-class	AtomicList-class
SimpleRleViewsList-class	RleViewsList-class
SimpleSplitDataFrameList-class	DataFrameList-class
SimpleViewsList	ViewsList-class
SimpleViewsList-class	ViewsList-class
simplify	RDApplyParams-class
simplify,RDApplyParams-method	RDApplyParams-class
simplify<-	RDApplyParams-class
simplify<-,RDApplyParams-method	RDApplyParams-class
slice	slice-methods
slice,Rle-method	slice-methods
slice,RleList-method	slice-methods
slice-methods	slice-methods
smoothEnds,CompressedIntegerList-method	AtomicList-class
smoothEnds,NumericList-method	AtomicList-class
smoothEnds,Rle-method	Rle-class
smoothEnds,RleList-method	AtomicList-class
smoothEnds,SimpleIntegerList-method	AtomicList-class
solveUserSEW	IRanges-constructor
solveUserSEW0	IRanges-constructor
sort,Rle-method	Rle-class
sort,RleList-method	AtomicList-class
sort,Vector-method	Vector-comparison
sort.Rle	Rle-class
sort.RleList	AtomicList-class
sort.Vector	Vector-comparison
space	RangesList-class
space,CompressedHitsList-method	HitsList-class
space,HitsList-method	HitsList-class
space,RangedData-method	RangedData-class
space,RangesList-method	RangesList-class
space,RangesMapping-method	RangesMapping-class
split,ANY,Vector-method	Vector-class
split,list,Vector-method	Vector-class
split,RangedData,ANY-method	RangedData-class
split,Vector,ANY-method	Vector-class
split,Vector,Vector-method	Vector-class
split<-,Vector-method	Vector-class
SplitDataFrameList	DataFrameList-class
SplitDataFrameList-class	DataFrameList-class
splitRanges	Rle-class
splitRanges,Rle-method	Rle-class
splitRanges,vectorORfactor-method	Rle-class
stack,DataFrameList-method	DataFrameList-class
stack,List-method	List-class
stack,RangedDataList-method	RangedDataList-class
start,CompressedIRangesList-method	IRangesList-class
start,GappedRanges-method	GappedRanges-class
start,IntervalForest-method	IntervalForest-class
start,IntervalTree-method	IntervalTree-class
start,IRanges-method	IRanges-class
start,PartitioningByEnd-method	Grouping-class
start,PartitioningByWidth-method	Grouping-class
start,RangedData-method	RangedData-class
start,Ranges-method	Ranges-class
start,RangesList-method	RangesList-class
start,Rle-method	Rle-class
start,SimpleViewsList-method	ViewsList-class
start,Views-method	Views-class
start<-	Ranges-class
start<-,IRanges-method	IRanges-class
start<-,RangedData-method	RangedData-class
start<-,RangesList-method	RangesList-class
start<-,Views-method	Views-class
strsplitAsListOfIntegerVectors	strutils
sub,ANY,ANY,CompressedCharacterList-method	AtomicList-class
sub,ANY,ANY,CompressedRleList-method	AtomicList-class
sub,ANY,ANY,Rle-method	Rle-class
sub,ANY,ANY,SimpleCharacterList-method	AtomicList-class
sub,ANY,ANY,SimpleRleList-method	AtomicList-class
subject	Views-class
subject,SimpleRleViewsList-method	RleViewsList-class
subject,Views-method	Views-class
subjectHits	Hits-class
subjectHits,CompressedHitsList-method	HitsList-class
subjectHits,Hits-method	Hits-class
subjectHits,HitsList-method	HitsList-class
subjectHits,RangesMapping-method	RangesMapping-class
subjectLength	Hits-class
subjectLength,CompressedHitsList-method	HitsList-class
subjectLength,Hits-method	Hits-class
subset,DataTable-method	DataTable-API
subset,Vector-method	Vector-class
subsetByFilter	FilterRules-class
subsetByFilter,ANY,FilterRules-method	FilterRules-class
subsetByOverlaps	findOverlaps-methods
subsetByOverlaps,RangedData,RangedData-method	findOverlaps-methods
subsetByOverlaps,RangedData,RangesList-method	findOverlaps-methods
subsetByOverlaps,RangesList,RangedData-method	findOverlaps-methods
subsetByOverlaps,Vector,Vector-method	findOverlaps-methods
substr,Rle-method	Rle-class
substring,Rle-method	Rle-class
subviews	Views-class
subviews,Views-method	Views-class
successiveIRanges	IRanges-utils
successiveViews	Views-class
sum,CompressedIntegerList-method	AtomicList-class
sum,CompressedLogicalList-method	AtomicList-class
sum,CompressedNumericList-method	AtomicList-class
sum,Views-method	view-summarization-methods
Summary,AtomicList-method	AtomicList-class
summary,CompressedIRangesList-method	IRangesList-class
Summary,CompressedRleList-method	AtomicList-class
summary,FilterMatrix-method	FilterMatrix-class
summary,FilterRules-method	FilterRules-class
Summary,Rle-method	Rle-class
summary,Rle-method	Rle-class
Summary,Views-method	view-summarization-methods
summary.Rle	Rle-class
svn.time	strutils
t,Hits-method	Hits-class
t,HitsList-method	HitsList-class
table,CompressedAtomicList-method	AtomicList-class
table,Rle-method	Rle-class
table,SimpleAtomicList-method	AtomicList-class
table,Vector-method	Vector-comparison
tail,Vector-method	Vector-class
tail.Vector	Vector-class
tapply,ANY,Vector-method	Vector-class
tapply,Vector,ANY-method	Vector-class
tapply,Vector,Vector-method	Vector-class
threebands	intra-range-methods
threebands,IRanges-method	intra-range-methods
tofactor	Grouping-class
togroup	Grouping-class
togroup,ANY-method	Grouping-class
togroup,H2LGrouping-method	Grouping-class
togrouplength	Grouping-class
togrouplength,Grouping-method	Grouping-class
togrouprank	Grouping-class
togrouprank,H2LGrouping-method	Grouping-class
tolower,CompressedCharacterList-method	AtomicList-class
tolower,CompressedRleList-method	AtomicList-class
tolower,Rle-method	Rle-class
tolower,SimpleCharacterList-method	AtomicList-class
tolower,SimpleRleList-method	AtomicList-class
toupper,CompressedCharacterList-method	AtomicList-class
toupper,CompressedRleList-method	AtomicList-class
toupper,Rle-method	Rle-class
toupper,SimpleCharacterList-method	AtomicList-class
toupper,SimpleRleList-method	AtomicList-class
trim	Views-class
trim,Views-method	Views-class
tseqapply	seqapply
union,CompressedIRangesList,CompressedIRangesList-method	setops-methods
union,Hits,Hits-method	setops-methods
union,IRanges,IRanges-method	setops-methods
union,RangesList,RangesList-method	setops-methods
unique,CompressedAtomicList-method	AtomicList-class
unique,CompressedRleList-method	AtomicList-class
unique,DataTable-method	DataTable-API
unique,Rle-method	Rle-class
unique,SimpleRleList-method	AtomicList-class
unique,Vector-method	Vector-comparison
unique.CompressedAtomicList	AtomicList-class
unique.CompressedRleList	AtomicList-class
unique.DataTable	DataTable-API
unique.Rle	Rle-class
unique.SimpleRleList	AtomicList-class
unique.Vector	Vector-comparison
universe	RangesList-class
universe,RangedData-method	RangedData-class
universe,RangesList-method	RangesList-class
universe,ViewsList-method	ViewsList-class
universe<-	RangesList-class
universe<-,RangedData-method	RangedData-class
universe<-,RangesList-method	RangesList-class
universe<-,ViewsList-method	ViewsList-class
unlist,CompressedList-method	SimpleList-class
unlist,IRangesList-method	IRangesList-class
unlist,List-method	List-class
unlist,RangedDataList-method	RangedDataList-class
unlist,Ranges-method	Ranges-class
unlist,SimpleNormalIRangesList-method	IRangesList-class
unsplit,List-method	List-class
update,IRanges-method	IRanges-class
update,Ranges-method	Ranges-class
updateObject,AnnotatedList-method	updateObject-methods
updateObject,CharacterList-method	updateObject-methods
updateObject,ComplexList-method	updateObject-methods
updateObject,FilterRules-method	updateObject-methods
updateObject,IntegerList-method	updateObject-methods
updateObject,IntervalTree-method	updateObject-methods
updateObject,IRanges-method	updateObject-methods
updateObject,IRangesList-method	updateObject-methods
updateObject,LogicalList-method	updateObject-methods
updateObject,MaskCollection-method	updateObject-methods
updateObject,NormalIRanges-method	updateObject-methods
updateObject,NumericList-method	updateObject-methods
updateObject,RangedData-method	updateObject-methods
updateObject,RangedDataList-method	updateObject-methods
updateObject,RangesList-method	updateObject-methods
updateObject,RawList-method	updateObject-methods
updateObject,RDApplyParams-method	updateObject-methods
updateObject,Rle-method	updateObject-methods
updateObject,RleList-method	updateObject-methods
updateObject,RleViews-method	updateObject-methods
updateObject,SplitXDataFrameList-method	updateObject-methods
updateObject,XDataFrame-method	updateObject-methods
updateObject,XDataFrameList-method	updateObject-methods
updateObject-methods	updateObject-methods
values	Vector-class
values,RangedData-method	RangedData-class
values,Vector-method	Vector-class
values<-	Vector-class
values<-,RangedData-method	RangedData-class
values<-,Vector-method	Vector-class
var,AtomicList,AtomicList-method	AtomicList-class
var,AtomicList,missing-method	AtomicList-class
var,Rle,missing-method	Rle-class
var,Rle,Rle-method	Rle-class
Vector	Vector-class
Vector-class	Vector-class
Vector-comparison	Vector-comparison
view-summarization-methods	view-summarization-methods
viewApply	view-summarization-methods
viewApply,RleViews-method	view-summarization-methods
viewApply,RleViewsList-method	view-summarization-methods
viewApply,Views-method	view-summarization-methods
viewMaxs	view-summarization-methods
viewMaxs,RleViews-method	view-summarization-methods
viewMaxs,RleViewsList-method	view-summarization-methods
viewMeans	view-summarization-methods
viewMeans,RleViews-method	view-summarization-methods
viewMeans,RleViewsList-method	view-summarization-methods
viewMins	view-summarization-methods
viewMins,RleViews-method	view-summarization-methods
viewMins,RleViewsList-method	view-summarization-methods
viewRangeMaxs	view-summarization-methods
viewRangeMaxs,RleViews-method	view-summarization-methods
viewRangeMaxs,RleViewsList-method	view-summarization-methods
viewRangeMins	view-summarization-methods
viewRangeMins,RleViews-method	view-summarization-methods
viewRangeMins,RleViewsList-method	view-summarization-methods
Views	Views-class
Views,Rle-method	RleViews-class
Views,RleList-method	RleViewsList-class
Views-class	Views-class
ViewsList	ViewsList-class
ViewsList-class	ViewsList-class
viewSums	view-summarization-methods
viewSums,RleViews-method	view-summarization-methods
viewSums,RleViewsList-method	view-summarization-methods
viewWhichMaxs	view-summarization-methods
viewWhichMaxs,RleViews-method	view-summarization-methods
viewWhichMaxs,RleViewsList-method	view-summarization-methods
viewWhichMins	view-summarization-methods
viewWhichMins,RleViews-method	view-summarization-methods
viewWhichMins,RleViewsList-method	view-summarization-methods
vmembers	Grouping-class
vmembers,Grouping-method	Grouping-class
vmembers,H2LGrouping-method	Grouping-class
which,CompressedLogicalList-method	AtomicList-class
which,CompressedRleList-method	AtomicList-class
which,Rle-method	Rle-class
which,SimpleLogicalList-method	AtomicList-class
which,SimpleRleList-method	AtomicList-class
which.max,CompressedRleList-method	AtomicList-class
which.max,Rle-method	Rle-class
which.max,Views-method	view-summarization-methods
which.min,CompressedRleList-method	AtomicList-class
which.min,Views-method	view-summarization-methods
whichAsIRanges	IRanges-utils
whichFirstNotNormal	Ranges-class
whichFirstNotNormal,Ranges-method	Ranges-class
whichFirstNotNormal,RangesList-method	IRangesList-class
width	Ranges-class
width,CompressedIRangesList-method	IRangesList-class
width,IntervalForest-method	IntervalForest-class
width,IRanges-method	IRanges-class
width,MaskCollection-method	MaskCollection-class
width,PartitioningByEnd-method	Grouping-class
width,PartitioningByWidth-method	Grouping-class
width,RangedData-method	RangedData-class
width,Ranges-method	Ranges-class
width,RangesList-method	RangesList-class
width,Rle-method	Rle-class
width,SimpleViewsList-method	ViewsList-class
width,Views-method	Views-class
width<-	Ranges-class
width<-,IRanges-method	IRanges-class
width<-,RangedData-method	RangedData-class
width<-,RangesList-method	RangesList-class
width<-,Views-method	Views-class
window,factor-method	Vector-class
window,NULL-method	Vector-class
window,Rle-method	Rle-class
window,Vector-method	Vector-class
window,vector-method	Vector-class
window.factor	Vector-class
window.NULL	Vector-class
window.Rle	Rle-class
window.Vector	Vector-class
window.vector	Vector-class
window<-,DataTable-method	DataTable-API
window<-,factor-method	Vector-class
window<-,Vector-method	Vector-class
window<-,vector-method	Vector-class
window<-.DataTable	DataTable-API
window<-.factor	Vector-class
window<-.Vector	Vector-class
window<-.vector	Vector-class
with,List-method	List-class
within,List-method	List-class
within,RangedData-method	RangedData-class
xtabs,DataTable-method	DataTable-stats
[,CompressedIRangesList-method	IRangesList-class
[,CompressedList-method	SimpleList-class
[,CompressedSplitDataFrameList-method	DataFrameList-class
[,DataFrame-method	DataFrame-class
[,FilterMatrix-method	FilterMatrix-class
[,FilterRules-method	FilterRules-class
[,IntervalForest-method	IntervalForest-class
[,List-method	List-class
[,MaskCollection-method	MaskCollection-class
[,RangedData-method	RangedData-class
[,RangesList-method	RangesList-class
[,Rle-method	Rle-class
[,SimpleIRangesList-method	IRangesList-class
[,SimpleList-method	SimpleList-class
[,SimpleRangesList-method	RangesList-class
[,SimpleSplitDataFrameList-method	DataFrameList-class
[,Vector-method	Vector-class
[<-,DataFrame-method	DataFrame-class
[<-,List-method	List-class
[<-,Rle-method	Rle-class
[<-,SplitDataFrameList-method	DataFrameList-class
[<-,Vector-method	Vector-class
[[,List-method	List-class
[[,RangedData-method	RangedData-class
[[<-,CompressedList-method	SimpleList-class
[[<-,DataFrame-method	DataFrame-class
[[<-,FilterRules-method	FilterRules-class
[[<-,List-method	List-class
[[<-,RangedData-method	RangedData-class
[[<-,SimpleList-method	SimpleList-class
