Infrastructure for manipulating intervals on sequences

Documentation for package ‘IRanges’ version 1.4.16

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-- --

!,CompressedLogicalList-method	Lists of Atomic Vectors in Natural and Rle Form
!,Rle-method	Rle objects
!,SimpleLogicalList-method	Lists of Atomic Vectors in Natural and Rle Form
!=	Ranges comparison
!=,DataTable,DataTable-method	DataTable objects
!=,integer,XIntegerViews-method	The XIntegerViews class
!=,Ranges,Ranges-method	Ranges comparison
!=,Sequence,Sequence-method	Sequence objects
!=,XInteger,XIntegerViews-method	The XIntegerViews class
!=,XIntegerViews,integer-method	The XIntegerViews class
!=,XIntegerViews,XInteger-method	The XIntegerViews class
!=,XIntegerViews,XIntegerViews-method	The XIntegerViews class
$,Sequence-method	Sequence objects
$<-,CompressedList-method	Simple and Compressed List Classes
$<-,RangedData-method	Data on ranges
$<-,SimpleList-method	Simple and Compressed List Classes
%in%,RangedData,RangedData-method	Interval Search Trees
%in%,RangedData,RangesList-method	Interval Search Trees
%in%,Ranges,Ranges-method	Interval Search Trees
%in%,RangesList,RangedData-method	Interval Search Trees
%in%,RangesList,RangesList-method	Interval Search Trees
%in%,Rle,ANY-method	Rle objects
<	Ranges comparison
<,Ranges,Ranges-method	Ranges comparison
<=	Ranges comparison
<=,Ranges,Ranges-method	Ranges comparison
==	Ranges comparison
==,integer,XIntegerViews-method	The XIntegerViews class
==,Ranges,Ranges-method	Ranges comparison
==,XDouble,XDouble-method	XVector objects
==,XInteger,XInteger-method	XVector objects
==,XInteger,XIntegerViews-method	The XIntegerViews class
==,XIntegerViews,integer-method	The XIntegerViews class
==,XIntegerViews,XInteger-method	The XIntegerViews class
==,XIntegerViews,XIntegerViews-method	The XIntegerViews class
>	Ranges comparison
>,Ranges,Ranges-method	Ranges comparison
>=	Ranges comparison
>=,Ranges,Ranges-method	Ranges comparison

-- A --

active	MaskCollection objects
active,FilterRules-method	Collection of Filter Rules
active,MaskCollection-method	MaskCollection objects
active<-	MaskCollection objects
active<-,FilterRules-method	Collection of Filter Rules
active<-,MaskCollection-method	MaskCollection objects
aggregate,CompressedList-method	Simple and Compressed List Classes
aggregate,data.frame-method	Sequence objects
aggregate,DataTable-method	DataTable objects
aggregate,matrix-method	Sequence objects
aggregate,Rle-method	Rle objects
aggregate,Sequence-method	Sequence objects
aggregate,SimpleList-method	Simple and Compressed List Classes
aggregate,ts-method	Sequence objects
aggregate,vector-method	Sequence objects
Annotated	Annotated class
Annotated-class	Annotated class
append,FilterRules,FilterRules-method	Collection of Filter Rules
append,MaskCollection,MaskCollection-method	MaskCollection objects
append,Sequence,Sequence-method	Sequence objects
applyFun	Applying over spaces
applyFun,RDApplyParams-method	Applying over spaces
applyFun<-	Applying over spaces
applyFun<-,RDApplyParams-method	Applying over spaces
applyParams	Applying over spaces
applyParams,RDApplyParams-method	Applying over spaces
applyParams<-	Applying over spaces
applyParams<-,RDApplyParams-method	Applying over spaces
as.character,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.character,Rle-method	Rle objects
as.complex,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.complex,Rle-method	Rle objects
as.data.frame,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.data.frame,DataFrame-method	External Data Frame
as.data.frame,GroupedIRanges-method	XVectorList objects
as.data.frame,RangedData-method	Data on ranges
as.data.frame,Ranges-method	Ranges objects
as.data.frame,RangesList-method	List of Ranges
as.data.frame,SplitDataFrameList-method	List of DataFrames
as.env	Sequence objects
as.env,DataTable-method	DataTable objects
as.env,RangedData-method	Data on ranges
as.env,Sequence-method	Sequence objects
as.factor,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.factor,Rle-method	Rle objects
as.integer,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.integer,Ranges-method	Ranges objects
as.integer,Rle-method	Rle objects
as.integer,XInteger-method	XVector objects
as.integer,XRaw-method	XVector objects
as.list,CompressedList-method	Simple and Compressed List Classes
as.list,Sequence-method	Sequence objects
as.list,SimpleList-method	Simple and Compressed List Classes
as.logical,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.logical,Rle-method	Rle objects
as.matrix,Ranges-method	Ranges objects
as.matrix,RangesMatching-method	Matchings between Ranges
as.matrix,RangesMatchingList-method	List of Matchings between Ranges
as.numeric,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.numeric,Rle-method	Rle objects
as.numeric,XDouble-method	XVector objects
as.numeric,XVector-method	XVector objects
as.raw,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
as.raw,Rle-method	Rle objects
as.raw,XRaw-method	XVector objects
as.table,RangesMatching-method	Matchings between Ranges
as.table,RangesMatchingList-method	List of Matchings between Ranges
as.vector,AtomicList,missing-method	Lists of Atomic Vectors in Natural and Rle Form
as.vector,Rle,missing-method	Rle objects
as.vector,XDouble,missing-method	XVector objects
as.vector,XInteger,missing-method	XVector objects
as.vector,XRaw,missing-method	XVector objects
asNormalIRanges	IRanges utility functions
AtomicList-class	Lists of Atomic Vectors in Natural and Rle Form

-- B --

Binning	Grouping objects
Binning-class	Grouping objects
by,DataTable-method	DataTable objects

-- C --

c,CompressedList-method	Simple and Compressed List Classes
c,FilterRules-method	Collection of Filter Rules
c,GroupedIRanges-method	XVectorList objects
c,IRanges-method	IRanges and NormalIRanges objects
c,RangedData-method	Data on ranges
c,Rle-method	Rle objects
c,Sequence-method	Sequence objects
c,SimpleList-method	Simple and Compressed List Classes
c,XRaw-method	XVector objects
c,XVectorList-method	XVectorList objects
cbind	DataTable objects
cbind,DataFrame-method	External Data Frame
cbind,DataFrameList-method	List of DataFrames
cbind,DataTable-method	DataTable objects
CharacterList	Lists of Atomic Vectors in Natural and Rle Form
CharacterList-class	Lists of Atomic Vectors in Natural and Rle Form
chartr,ANY,ANY,Rle-method	Rle objects
class:Binning	Grouping objects
class:DataTable	DataTable objects
class:Dups	Grouping objects
class:GroupedIRanges	XVectorList objects
class:Grouping	Grouping objects
class:H2LGrouping	Grouping objects
class:IRanges	IRanges and NormalIRanges objects
class:MaskCollection	MaskCollection objects
class:NormalIRanges	IRanges and NormalIRanges objects
class:Partitioning	Grouping objects
class:PartitioningByEnd	Grouping objects
class:PartitioningByWidth	Grouping objects
class:Ranges	Ranges objects
class:Rle	Rle objects
class:RleViews	The RleViews class
class:Sequence	Sequence objects
class:Views	Views objects
class:XDouble	XVector objects
class:XInteger	XVector objects
class:XIntegerViews	The XIntegerViews class
class:XRaw	XVector objects
class:XRawList	XVectorList objects
class:XVector	XVector objects
class:XVectorList	XVectorList objects
coerce,ANY,CompressedSplitDataFrameList-method	List of DataFrames
coerce,ANY,SimpleSplitDataFrameList-method	List of DataFrames
coerce,AtomicList,character-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,complex-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,CompressedSplitDataFrameList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,data.frame-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,factor-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,integer-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,logical-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,numeric-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,raw-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,SimpleSplitDataFrameList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,AtomicList,vector-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,character,Rle-method	Rle objects
coerce,complex,Rle-method	Rle objects
coerce,data.frame,DataFrame-method	External Data Frame
coerce,data.frame,RangedData-method	Data on ranges
coerce,DataFrame,data.frame-method	External Data Frame
coerce,DataTable,RangedData-method	Data on ranges
coerce,factor,Rle-method	Rle objects
coerce,integer,DataFrame-method	External Data Frame
coerce,integer,IRanges-method	IRanges and NormalIRanges objects
coerce,integer,Rle-method	Rle objects
coerce,integer,XVector-method	XVector objects
coerce,IntervalTree,IRanges-method	Interval Search Trees
coerce,IRanges,IntervalTree-method	Interval Search Trees
coerce,IRanges,NormalIRanges-method	IRanges utility functions
coerce,IRangesList,list-method	List of IRanges
coerce,IRangesList,NormalIRanges-method	List of IRanges
coerce,list,DataFrame-method	External Data Frame
coerce,logical,IRanges-method	IRanges and NormalIRanges objects
coerce,logical,NormalIRanges-method	IRanges and NormalIRanges objects
coerce,logical,Rle-method	Rle objects
coerce,LogicalList,CompressedIRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,LogicalList,IRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,LogicalList,SimpleIRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,MaskCollection,NormalIRanges-method	MaskCollection objects
coerce,matrix,DataFrame-method	External Data Frame
coerce,numeric,IRanges-method	IRanges and NormalIRanges objects
coerce,numeric,Rle-method	Rle objects
coerce,numeric,XDouble-method	XVector objects
coerce,numeric,XInteger-method	XVector objects
coerce,numeric,XRaw-method	XVector objects
coerce,numeric,XVector-method	XVector objects
coerce,RangedData,DataFrame-method	Data on ranges
coerce,Ranges,IntervalTree-method	Interval Search Trees
coerce,Ranges,IRanges-method	IRanges and NormalIRanges objects
coerce,Ranges,PartitioningByEnd-method	Grouping objects
coerce,Ranges,PartitioningByWidth-method	Grouping objects
coerce,Ranges,RangedData-method	Data on ranges
coerce,RangesList,CompressedIRangesList-method	List of Ranges
coerce,RangesList,RangedData-method	List of Ranges
coerce,RangesList,SimpleIRangesList-method	List of Ranges
coerce,raw,Rle-method	Rle objects
coerce,raw,XRaw-method	XVector objects
coerce,raw,XVector-method	XVector objects
coerce,Rle,character-method	Rle objects
coerce,Rle,complex-method	Rle objects
coerce,Rle,factor-method	Rle objects
coerce,Rle,integer-method	Rle objects
coerce,Rle,IRanges-method	Rle objects
coerce,Rle,logical-method	Rle objects
coerce,Rle,NormalIRanges-method	Rle objects
coerce,Rle,numeric-method	Rle objects
coerce,Rle,RangedData-method	Data on ranges
coerce,Rle,raw-method	Rle objects
coerce,Rle,vector-method	Rle objects
coerce,RleList,CompressedIRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,RleList,IRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,RleList,RangedData-method	Data on ranges
coerce,RleList,SimpleIRangesList-method	Lists of Atomic Vectors in Natural and Rle Form
coerce,Sequence,DataFrame-method	External Data Frame
coerce,Sequence,list-method	Sequence objects
coerce,Sequence,Views-method	Views objects
coerce,SplitDataFrameList,DataFrame-method	List of DataFrames
coerce,vector,DataFrame-method	External Data Frame
coerce,vector,Rle-method	Rle objects
coerce,Views,NormalIRanges-method	Views objects
collapse	MaskCollection objects
collapse,MaskCollection-method	MaskCollection objects
colnames,DataFrame-method	External Data Frame
colnames,DataFrameList-method	List of DataFrames
colnames,RangedData-method	Data on ranges
colnames<-,CompressedSplitDataFrameList-method	List of DataFrames
colnames<-,DataFrame-method	External Data Frame
colnames<-,RangedData-method	Data on ranges
colnames<-,SimpleDataFrameList-method	List of DataFrames
Complex,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Complex,Rle-method	Rle objects
Complex,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
ComplexList	Lists of Atomic Vectors in Natural and Rle Form
ComplexList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedAtomicList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedCharacterList	Lists of Atomic Vectors in Natural and Rle Form
CompressedCharacterList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedComplexList	Lists of Atomic Vectors in Natural and Rle Form
CompressedComplexList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedIntegerList	Lists of Atomic Vectors in Natural and Rle Form
CompressedIntegerList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedIRangesList-class	List of IRanges
CompressedList	Simple and Compressed List Classes
CompressedList-class	Simple and Compressed List Classes
CompressedLogicalList	Lists of Atomic Vectors in Natural and Rle Form
CompressedLogicalList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedNumericList	Lists of Atomic Vectors in Natural and Rle Form
CompressedNumericList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedRawList	Lists of Atomic Vectors in Natural and Rle Form
CompressedRawList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedRleList	Lists of Atomic Vectors in Natural and Rle Form
CompressedRleList-class	Lists of Atomic Vectors in Natural and Rle Form
CompressedSplitDataFrameList-class	List of DataFrames
cor,Rle,Rle-method	Rle objects
countOverlap	Interval Search Trees
countOverlaps	Interval Search Trees
countOverlaps,Ranges,Ranges-method	Interval Search Trees
cov,Rle,Rle-method	Rle objects
coverage	Coverage across a set of ranges
coverage,IRanges-method	Coverage across a set of ranges
coverage,MaskCollection-method	Coverage across a set of ranges
coverage,numeric-method	Coverage across a set of ranges
coverage,RangedData-method	Coverage across a set of ranges
coverage,RangesList-method	Coverage across a set of ranges
coverage,Views-method	Coverage across a set of ranges
coverage.getShift0FromStartEnd	Coverage across a set of ranges
coverage.getWidthFromStartEnd	Coverage across a set of ranges
coverage.isCalledWithStartEndInterface	Coverage across a set of ranges
coverage.normargWidth	Coverage across a set of ranges

-- D --

DataFrame	External Data Frame
DataFrame-class	External Data Frame
DataFrameList	List of DataFrames
DataFrameList-class	List of DataFrames
DataTable	DataTable objects
DataTable-class	DataTable objects
DataTable-stats	Statistical modeling with DataTable
DataTableORNULL-class	DataTable objects
desc	MaskCollection objects
desc,MaskCollection-method	MaskCollection objects
desc<-	MaskCollection objects
desc<-,MaskCollection-method	MaskCollection objects
diff,Rle-method	Rle objects
dim,DataFrameList-method	List of DataFrames
dim,DataTable-method	DataTable objects
dim,RangesMatching-method	Matchings between Ranges
dimnames,DataFrameList-method	List of DataFrames
dimnames,DataTable-method	DataTable objects
dimnames<-,DataFrameList-method	List of DataFrames
dimnames<-,DataTable-method	DataTable objects
disjoin	Making Ranges disjoint
disjoin,Ranges-method	Making Ranges disjoint
disjoin,RangesList-method	RangesList utility functions
disjointBins	Making Ranges disjoint
disjointBins,Ranges-method	Making Ranges disjoint
duplicated,Dups-method	Grouping objects
duplicated,Ranges-method	Ranges comparison
Dups	Grouping objects
Dups-class	Grouping objects

-- E --

elementLengths	Sequence objects
elementLengths,CompressedList-method	Sequence objects
elementLengths,list-method	Sequence objects
elementLengths,RangedData-method	Data on ranges
elementLengths,Sequence-method	Sequence objects
elementMetadata	Sequence objects
elementMetadata,Sequence-method	Sequence objects
elementMetadata<-	Sequence objects
elementMetadata<-,Sequence,DataTableORNULL-method	Sequence objects
elementType	Sequence objects
elementType,Sequence-method	Sequence objects
end,CompressedIRangesList-method	List of Ranges
end,IntervalTree-method	Interval Search Trees
end,PartitioningByEnd-method	Grouping objects
end,PartitioningByWidth-method	Grouping objects
end,RangedData-method	Data on ranges
end,Ranges-method	Ranges objects
end,RangesList-method	List of Ranges
end,Rle-method	Rle objects
end<-	Ranges objects
end<-,IRanges-method	IRanges and NormalIRanges objects
end<-,RangedData-method	Data on ranges
end<-,RangesList-method	List of Ranges
endoapply	Endomorphisms via application of a function over an object's elements
endoapply,CompressedList-method	Simple and Compressed List Classes
endoapply,data.frame-method	Endomorphisms via application of a function over an object's elements
endoapply,list-method	Endomorphisms via application of a function over an object's elements
endoapply,RangedData-method	Data on ranges
endoapply,Sequence-method	Sequence objects
endoapply,SimpleList-method	Simple and Compressed List Classes
eval,expressionORlanguage,Sequence-method	Sequence objects
eval,FilterRules,ANY-method	Collection of Filter Rules

-- F --

Filter,ANY,Sequence-method	Sequence objects
FilterRules	Collection of Filter Rules
filterRules	Applying over spaces
filterRules,RDApplyParams-method	Applying over spaces
FilterRules-class	Collection of Filter Rules
filterRules<-	Applying over spaces
filterRules<-,RDApplyParams-method	Applying over spaces
Find,ANY,Sequence-method	Sequence objects
findOverlaps	Interval Search Trees
findOverlaps,integer,Ranges-method	Interval Search Trees
findOverlaps,RangedData,RangedData-method	Interval Search Trees
findOverlaps,RangedData,RangesList-method	Interval Search Trees
findOverlaps,Ranges,IntervalTree-method	Interval Search Trees
findOverlaps,Ranges,missing-method	Interval Search Trees
findOverlaps,Ranges,Ranges-method	Interval Search Trees
findOverlaps,RangesList,RangedData-method	Interval Search Trees
findOverlaps,RangesList,RangesList-method	Interval Search Trees
findRange	Rle objects
findRange,Rle-method	Rle objects
findRun	Rle objects
findRun,Rle-method	Rle objects
first	Ranges objects
first,Ranges-method	Ranges objects
flank	IRanges utility functions
flank,CompressedIRangesList-method	RangesList utility functions
flank,Ranges-method	IRanges utility functions
flank,RangesList-method	RangesList utility functions
follow	Nearest neighbor finding
follow,Ranges,RangesORmissing-method	Nearest neighbor finding

-- G --

gaps	Set operations on IRanges objects
gaps,IRanges-method	Set operations on IRanges objects
gaps,MaskCollection-method	MaskCollection objects
gaps,Ranges-method	Set operations on IRanges objects
gaps,RangesList-method	RangesList utility functions
gaps,Views-method	Views objects
GroupedIRanges	XVectorList objects
GroupedIRanges-class	XVectorList objects
Grouping	Grouping objects
Grouping-class	Grouping objects
grouplength	Grouping objects
grouplength,Binning-method	Grouping objects
grouplength,Grouping-method	Grouping objects
grouplength,H2LGrouping-method	Grouping objects
grouplength,Partitioning-method	Grouping objects
grouprank	Grouping objects
grouprank,H2LGrouping-method	Grouping objects
gsub,ANY,ANY,Rle-method	Rle objects

-- H --

H2LGrouping	Grouping objects
H2LGrouping-class	Grouping objects
head,DataTable-method	DataTable objects
head,Sequence-method	Sequence objects
high2low	Grouping objects
high2low,ANY-method	Grouping objects
high2low,H2LGrouping-method	Grouping objects

-- I --

IntegerList	Lists of Atomic Vectors in Natural and Rle Form
IntegerList-class	Lists of Atomic Vectors in Natural and Rle Form
intersect,IRanges,IRanges-method	Set operations on IRanges objects
intersect,RangesList,RangesList-method	RangesList utility functions
IntervalTree	Interval Search Trees
IntervalTree-class	Interval Search Trees
intToAdjacentRanges	IRanges utility functions
intToRanges	IRanges utility functions
IQR,Rle-method	Rle objects
IRanges	The IRanges constructor and supporting functions
IRanges-class	IRanges and NormalIRanges objects
IRanges-constructor	The IRanges constructor and supporting functions
IRanges-setops	Set operations on IRanges objects
IRanges-utils	IRanges utility functions
IRangesList	List of IRanges
IRangesList-class	List of IRanges
is.na,Rle-method	Rle objects
isDisjoint	Ranges objects
isDisjoint,Ranges-method	Ranges objects
isEmpty	Sequence objects
isEmpty,ANY-method	Sequence objects
isEmpty,CompressedList-method	Simple and Compressed List Classes
isEmpty,NormalIRanges-method	IRanges and NormalIRanges objects
isEmpty,Ranges-method	Ranges objects
isEmpty,SimpleList-method	Simple and Compressed List Classes
isNormal	Ranges objects
isNormal,Ranges-method	Ranges objects

-- L --

lapply,CompressedList-method	Simple and Compressed List Classes
lapply,RangedData-method	Data on ranges
lapply,Sequence-method	Sequence objects
lapply,SimpleList-method	Simple and Compressed List Classes
last	Ranges objects
last,Ranges-method	Ranges objects
length,Binning-method	Grouping objects
length,CompressedList-method	Simple and Compressed List Classes
length,H2LGrouping-method	Grouping objects
length,IntervalTree-method	Interval Search Trees
length,MaskCollection-method	MaskCollection objects
length,PartitioningByEnd-method	Grouping objects
length,PartitioningByWidth-method	Grouping objects
length,RangedData-method	Data on ranges
length,Ranges-method	Ranges objects
length,RangesMatching-method	Matchings between Ranges
length,Rle-method	Rle objects
length,SimpleList-method	Simple and Compressed List Classes
length,XVector-method	XVector objects
length,XVectorList-method	XVectorList objects
length<-,H2LGrouping-method	Grouping objects
levels,Rle-method	Rle objects
levels<-,Rle-method	Rle objects
LogicalList	Lists of Atomic Vectors in Natural and Rle Form
LogicalList-class	Lists of Atomic Vectors in Natural and Rle Form
low2high	Grouping objects
low2high,H2LGrouping-method	Grouping objects

-- M --

mad,Rle-method	Rle objects
Map	Sequence objects
Map,Sequence-method	Sequence objects
mapply	Sequence objects
mapply,Sequence-method	Sequence objects
Mask	MaskCollection objects
MaskCollection	MaskCollection objects
MaskCollection-class	MaskCollection objects
MaskCollection.show_frame	MaskCollection objects
maskedratio	MaskCollection objects
maskedratio,MaskCollection-method	MaskCollection objects
maskedwidth	MaskCollection objects
maskedwidth,MaskCollection-method	MaskCollection objects
match,Ranges,Ranges-method	Interval Search Trees
match,RangesList,RangesList-method	Interval Search Trees
matchMatrix	Matchings between Ranges
matchMatrix,RangesMatching-method	Matchings between Ranges
Math,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Math,Rle-method	Rle objects
Math,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Math2,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Math2,Rle-method	Rle objects
Math2,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
max,MaskCollection-method	MaskCollection objects
max,NormalIRanges-method	IRanges and NormalIRanges objects
mean,Rle-method	Rle objects
median,Rle-method	Rle objects
members	Grouping objects
members,Grouping-method	Grouping objects
members,H2LGrouping-method	Grouping objects
mendoapply	Endomorphisms via application of a function over an object's elements
mendoapply,CompressedList-method	Simple and Compressed List Classes
mendoapply,data.frame-method	Endomorphisms via application of a function over an object's elements
mendoapply,list-method	Endomorphisms via application of a function over an object's elements
mendoapply,Sequence-method	Sequence objects
mendoapply,SimpleList-method	Simple and Compressed List Classes
metadata	Annotated class
metadata,Annotated-method	Annotated class
metadata<-	Annotated class
metadata<-,Annotated,list-method	Annotated class
mid	Ranges objects
mid,Ranges-method	Ranges objects
min,MaskCollection-method	MaskCollection objects
min,NormalIRanges-method	IRanges and NormalIRanges objects

-- N --

names,Binning-method	Grouping objects
names,CompressedList-method	Simple and Compressed List Classes
names,IRanges-method	IRanges and NormalIRanges objects
names,MaskCollection-method	MaskCollection objects
names,Partitioning-method	Grouping objects
names,RangedData-method	Data on ranges
names,SimpleList-method	Simple and Compressed List Classes
names,XVectorList-method	XVectorList objects
names<-,Binning-method	Grouping objects
names<-,CompressedList-method	Simple and Compressed List Classes
names<-,IRanges-method	IRanges and NormalIRanges objects
names<-,MaskCollection-method	MaskCollection objects
names<-,Partitioning-method	Grouping objects
names<-,RangedData-method	Data on ranges
names<-,SimpleList-method	Simple and Compressed List Classes
names<-,XVectorList-method	XVectorList objects
narrow	IRanges utility functions
narrow,CompressedIRangesList-method	RangesList utility functions
narrow,IRanges-method	IRanges utility functions
narrow,NormalIRanges-method	IRanges utility functions
narrow,Ranges-method	IRanges utility functions
narrow,RangesList-method	RangesList utility functions
narrow,XVectorList-method	XVectorList objects
nchar,Rle-method	Rle objects
ncol,DataFrame-method	External Data Frame
ncol,DataFrameList-method	List of DataFrames
NCOL,DataTable-method	DataTable objects
ncol,RangedData-method	Data on ranges
nearest	Nearest neighbor finding
nearest,Ranges,RangesORmissing-method	Nearest neighbor finding
newViews	Views objects
nir_list	MaskCollection objects
nir_list,MaskCollection-method	MaskCollection objects
nobj	Grouping objects
nobj,Binning-method	Grouping objects
nobj,H2LGrouping-method	Grouping objects
nobj,PartitioningByEnd-method	Grouping objects
nobj,PartitioningByWidth-method	Grouping objects
NormalIRanges	IRanges and NormalIRanges objects
NormalIRanges-class	IRanges and NormalIRanges objects
nrow,DataFrame-method	External Data Frame
nrow,DataFrameList-method	List of DataFrames
NROW,DataTable-method	DataTable objects
nrow,RangedData-method	Data on ranges
nrun	Rle objects
nrun,Rle-method	Rle objects
NumericList	Lists of Atomic Vectors in Natural and Rle Form
NumericList-class	Lists of Atomic Vectors in Natural and Rle Form

-- O --

Ops,atomic,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,atomic,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,AtomicList,atomic-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,CompressedAtomicList,atomic-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,CompressedAtomicList,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,CompressedAtomicList,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,Ranges,numeric-method	Ranges objects
Ops,RangesList,ANY-method	List of Ranges
Ops,Rle,Rle-method	Rle objects
Ops,Rle,vector-method	Rle objects
Ops,SimpleAtomicList,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,SimpleAtomicList,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
Ops,vector,Rle-method	Rle objects
order	Ranges comparison
order,Ranges-method	Ranges comparison
overlap	Interval Search Trees

-- P --

Partitioning	Grouping objects
Partitioning-class	Grouping objects
PartitioningByEnd	Grouping objects
PartitioningByEnd-class	Grouping objects
PartitioningByWidth	Grouping objects
PartitioningByWidth-class	Grouping objects
pgap	Set operations on IRanges objects
pgap,IRanges,IRanges-method	Set operations on IRanges objects
pintersect	Set operations on IRanges objects
pintersect,IRanges,IRanges-method	Set operations on IRanges objects
pmax	Rle objects
pmax,Rle-method	Rle objects
pmax.int	Rle objects
pmax.int,Rle-method	Rle objects
pmin	Rle objects
pmin,Rle-method	Rle objects
pmin.int	Rle objects
pmin.int,Rle-method	Rle objects
Position,ANY,Sequence-method	Sequence objects
precede	Nearest neighbor finding
precede,Ranges,RangesORmissing-method	Nearest neighbor finding
psetdiff	Set operations on IRanges objects
psetdiff,IRanges,IRanges-method	Set operations on IRanges objects
punion	Set operations on IRanges objects
punion,IRanges,IRanges-method	Set operations on IRanges objects

-- Q --

quantile,Rle-method	Rle objects
queryHits	Matchings between Ranges
queryHits,RangesMatching-method	Matchings between Ranges
queryHits,RangesMatchingList-method	List of Matchings between Ranges

-- R --

range,RangedData-method	RangedData utility functions
range,Ranges-method	IRanges utility functions
range,RangesList-method	RangesList utility functions
RangedData	Data on ranges
rangedData	Applying over spaces
rangedData,RDApplyParams-method	Applying over spaces
RangedData-class	Data on ranges
RangedData-utils	RangedData utility functions
rangedData<-	Applying over spaces
rangedData<-,RDApplyParams-method	Applying over spaces
RangedDataList	Lists of RangedData
RangedDataList-class	Lists of RangedData
Ranges	Ranges objects
ranges	Data on ranges
ranges,RangedData-method	Data on ranges
ranges,RangesMatching-method	Matchings between Ranges
ranges,RangesMatchingList-method	List of Matchings between Ranges
Ranges-class	Ranges objects
Ranges-comparison	Ranges comparison
ranges<-	Data on ranges
ranges<-,RangedData-method	Data on ranges
RangesList	List of Ranges
RangesList-class	List of Ranges
RangesList-utils	RangesList utility functions
RangesMatching-class	Matchings between Ranges
RangesMatchingList-class	List of Matchings between Ranges
RangesORmissing-class	Ranges objects
rank,Ranges-method	Ranges comparison
RawList	Lists of Atomic Vectors in Natural and Rle Form
RawList-class	Lists of Atomic Vectors in Natural and Rle Form
rbind	DataTable objects
rbind,DataFrame-method	External Data Frame
rbind,DataFrameList-method	List of DataFrames
rbind,DataTable-method	DataTable objects
rbind,RangedData-method	Data on ranges
rdapply	Applying over spaces
rdapply,RDApplyParams-method	Applying over spaces
RDApplyParams	Applying over spaces
RDApplyParams-class	Applying over spaces
read.agpMask	Read a mask from a file
read.gapMask	Read a mask from a file
read.liftMask	Read a mask from a file
read.Mask	Read a mask from a file
read.rmMask	Read a mask from a file
read.trfMask	Read a mask from a file
reduce	IRanges utility functions
Reduce,ANY,Sequence-method	Sequence objects
reduce,IRanges-method	IRanges utility functions
reduce,RangedData-method	Data on ranges
reduce,Ranges-method	IRanges utility functions
reduce,RangesList-method	RangesList utility functions
reducerFun	Applying over spaces
reducerFun,RDApplyParams-method	Applying over spaces
reducerFun<-	Applying over spaces
reducerFun<-,RDApplyParams-method	Applying over spaces
reducerParams	Applying over spaces
reducerParams,RDApplyParams-method	Applying over spaces
reducerParams<-	Applying over spaces
reducerParams<-,RDApplyParams-method	Applying over spaces
reflect	IRanges utility functions
reflect,Ranges-method	IRanges utility functions
rep,Rle-method	Rle objects
rep,Sequence-method	Sequence objects
rep.int	Rle objects
rep.int,Rle-method	Rle objects
resize	IRanges utility functions
resize,CompressedIRangesList-method	RangesList utility functions
resize,IRanges-method	IRanges utility functions
resize,NormalIRanges-method	IRanges utility functions
resize,Ranges-method	IRanges utility functions
resize,RangesList-method	RangesList utility functions
restrict	IRanges utility functions
restrict,CompressedIRangesList-method	RangesList utility functions
restrict,IRanges-method	IRanges utility functions
restrict,Ranges-method	IRanges utility functions
restrict,RangesList-method	RangesList utility functions
rev,Rle-method	Rle objects
rev,Sequence-method	Sequence objects
reverse	Reverse an IRanges object
reverse,IRanges-method	Reverse an IRanges object
reverse,MaskCollection-method	Reverse an IRanges object
reverse,NormalIRanges-method	Reverse an IRanges object
reverse,SharedRaw-method	Reverse an IRanges object
reverse,SharedVector_Pool-method	Reverse an IRanges object
Rle	Rle objects
Rle,missing,missing-method	Rle objects
Rle,vectorORfactor,integer-method	Rle objects
Rle,vectorORfactor,missing-method	Rle objects
Rle,vectorORfactor,numeric-method	Rle objects
Rle-class	Rle objects
RleList	Lists of Atomic Vectors in Natural and Rle Form
RleList-class	Lists of Atomic Vectors in Natural and Rle Form
RleViews	The RleViews class
RleViews-class	The RleViews class
RleViewsList	List of RleViews
RleViewsList-class	List of RleViews
rownames,DataFrame-method	External Data Frame
rownames,DataFrameList-method	List of DataFrames
rownames,RangedData-method	Data on ranges
rownames<-,CompressedSplitDataFrameList-method	List of DataFrames
rownames<-,DataFrame-method	External Data Frame
rownames<-,RangedData-method	Data on ranges
rownames<-,SimpleDataFrameList-method	List of DataFrames
runLength	Rle objects
runLength,Rle-method	Rle objects
runLength<-	Rle objects
runLength<-,Rle-method	Rle objects
runmean	Fixed width running window summaries across vector-like objects
runmean,Rle-method	Rle objects
runmean,RleList-method	Lists of Atomic Vectors in Natural and Rle Form
runmed,Rle-method	Rle objects
runmed,RleList-method	Lists of Atomic Vectors in Natural and Rle Form
runq	Fixed width running window summaries across vector-like objects
runq,Rle-method	Rle objects
runq,RleList-method	Lists of Atomic Vectors in Natural and Rle Form
runstat	Fixed width running window summaries across vector-like objects
runsum	Fixed width running window summaries across vector-like objects
runsum,Rle-method	Rle objects
runsum,RleList-method	Lists of Atomic Vectors in Natural and Rle Form
runValue	Rle objects
runValue,Rle-method	Rle objects
runValue<-	Rle objects
runValue<-,Rle-method	Rle objects
runwtsum	Fixed width running window summaries across vector-like objects
runwtsum,Rle-method	Rle objects
runwtsum,RleList-method	Lists of Atomic Vectors in Natural and Rle Form

-- S --

safeExplode	Low-level string utilities
sapply,Sequence-method	Sequence objects
score	Score accessor and setter
score,AlignmentSpace-method	Alignments between sequences
score,RangedData-method	Data on ranges
score<-	Score accessor and setter
score<-,RangedData-method	Data on ranges
sd,Rle-method	Rle objects
seqextract	Sequence objects
seqselect	Sequence objects
seqselect,CompressedList-method	Simple and Compressed List Classes
seqselect,DataTable-method	DataTable objects
seqselect,GroupedIRanges-method	XVectorList objects
seqselect,IRanges-method	IRanges and NormalIRanges objects
seqselect,RangedData-method	Data on ranges
seqselect,Rle-method	Rle objects
seqselect,Sequence-method	Sequence objects
seqselect,SimpleList-method	Simple and Compressed List Classes
seqselect,vector-method	Sequence objects
seqselect,XVector-method	XVector objects
seqselect,XVectorList-method	XVectorList objects
seqselect<-	Sequence objects
seqselect<-,CompressedAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
seqselect<-,CompressedList-method	Simple and Compressed List Classes
seqselect<-,DataTable-method	DataTable objects
seqselect<-,RangedData-method	Data on ranges
seqselect<-,Rle-method	Rle objects
seqselect<-,Sequence-method	Sequence objects
seqselect<-,SimpleAtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
seqselect<-,SimpleList-method	Simple and Compressed List Classes
seqselect<-,vector-method	Sequence objects
Sequence	Sequence objects
Sequence-class	Sequence objects
setdiff,IRanges,IRanges-method	Set operations on IRanges objects
setdiff,RangesList,RangesList-method	RangesList utility functions
shift	IRanges utility functions
shift,CompressedIRangesList-method	RangesList utility functions
shift,IRanges-method	IRanges utility functions
shift,Ranges-method	IRanges utility functions
shift,RangesList-method	RangesList utility functions
shiftApply	Sequence objects
shiftApply,Rle,Rle-method	Rle objects
shiftApply,Sequence,Sequence-method	Sequence objects
shiftApply,vector,vector-method	Sequence objects
show,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
show,CompressedList-method	Simple and Compressed List Classes
show,DataTable-method	DataTable objects
show,Dups-method	Grouping objects
show,GroupedIRanges-method	XVectorList objects
show,Grouping-method	Grouping objects
show,IRangesList-method	List of Ranges
show,MaskCollection-method	MaskCollection objects
show,RangedData-method	Data on ranges
show,Ranges-method	Ranges objects
show,RangesList-method	List of Ranges
show,Rle-method	Rle objects
show,RleList-method	Lists of Atomic Vectors in Natural and Rle Form
show,RleViews-method	The RleViews class
show,SimpleList-method	Simple and Compressed List Classes
show,SplitDataFrameList-method	List of DataFrames
show,XDouble-method	XVector objects
show,XIntegerViews-method	The XIntegerViews class
show,XVector-method	XVector objects
SimpleAtomicList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList	Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList	Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleDataFrameList-class	List of DataFrames
SimpleIntegerList	Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleIRangesList-class	List of IRanges
SimpleList	Simple and Compressed List Classes
SimpleList-class	Simple and Compressed List Classes
SimpleLogicalList	Lists of Atomic Vectors in Natural and Rle Form
SimpleLogicalList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList	Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRangesList-class	List of Ranges
SimpleRawList	Lists of Atomic Vectors in Natural and Rle Form
SimpleRawList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleViewsList-class	List of RleViews
SimpleSplitDataFrameList-class	List of DataFrames
simplify	Applying over spaces
simplify,RDApplyParams-method	Applying over spaces
simplify<-	Applying over spaces
simplify<-,RDApplyParams-method	Applying over spaces
slice	Utility functions and numeric summary of Views of numerics
slice,integer-method	Utility functions and numeric summary of Views of numerics
slice,Rle-method	Utility functions and numeric summary of Views of numerics
slice,RleList-method	Utility functions and numeric summary of Views of numerics
slice,XInteger-method	Utility functions and numeric summary of Views of numerics
smoothEnds,Rle-method	Rle objects
solveUserSEW	The IRanges constructor and supporting functions
solveUserSEW0	The IRanges constructor and supporting functions
sort,Ranges-method	Ranges comparison
sort,Rle-method	Rle objects
space	List of Ranges
space,RangedData-method	Data on ranges
space,RangesList-method	List of Ranges
space,RangesMatchingList-method	List of Matchings between Ranges
split,DataFrame-method	External Data Frame
split,IRanges-method	List of Ranges
split,RangedData-method	Data on ranges
split,Ranges-method	List of Ranges
split,Rle-method	Rle objects
SplitDataFrameList	List of DataFrames
SplitDataFrameList-class	List of DataFrames
start,CompressedIRangesList-method	List of Ranges
start,IntervalTree-method	Interval Search Trees
start,IRanges-method	IRanges and NormalIRanges objects
start,PartitioningByEnd-method	Grouping objects
start,PartitioningByWidth-method	Grouping objects
start,RangedData-method	Data on ranges
start,Ranges-method	Ranges objects
start,RangesList-method	List of Ranges
start,Rle-method	Rle objects
start<-	Ranges objects
start<-,IRanges-method	IRanges and NormalIRanges objects
start<-,RangedData-method	Data on ranges
start<-,RangesList-method	List of Ranges
strsplitAsListOfIntegerVectors	Low-level string utilities
sub,ANY,ANY,Rle-method	Rle objects
subject	Views objects
subject,SimpleRleViewsList-method	List of RleViews
subject,Views-method	Views objects
subjectHits	Matchings between Ranges
subjectHits,RangesMatching-method	Matchings between Ranges
subjectHits,RangesMatchingList-method	List of Matchings between Ranges
subseq	XVector objects
subseq,MaskCollection-method	MaskCollection objects
subseq,XVector-method	XVector objects
subseq,XVectorList-method	XVectorList objects
subseq<-	XVector objects
subseq<-,XVector-method	XVector objects
subset,DataTable-method	DataTable objects
subset,Sequence-method	Sequence objects
substr,Rle-method	Rle objects
substring,Rle-method	Rle objects
subviews	Views objects
subviews,Views-method	Views objects
successiveIRanges	IRanges utility functions
successiveViews	Views objects
Summary,AtomicList-method	Lists of Atomic Vectors in Natural and Rle Form
summary,CompressedIRangesList-method	List of IRanges
Summary,Rle-method	Rle objects
summary,Rle-method	Rle objects

-- T --

t,RangesMatching-method	Matchings between Ranges
t,RangesMatchingList-method	List of Matchings between Ranges
table	Rle objects
table,Rle-method	Rle objects
tail,DataTable-method	DataTable objects
tail,Sequence-method	Sequence objects
threebands	IRanges utility functions
threebands,IRanges-method	IRanges utility functions
threebands,XVectorList-method	XVectorList objects
togroup	Grouping objects
togroup,Binning-method	Grouping objects
togroup,H2LGrouping-method	Grouping objects
togroup,Partitioning-method	Grouping objects
togrouplength	Grouping objects
togrouplength,Grouping-method	Grouping objects
togrouprank	Grouping objects
togrouprank,H2LGrouping-method	Grouping objects
tolower,Rle-method	Rle objects
toNormalIRanges	IRanges utility functions
toupper,Rle-method	Rle objects
trim	Views objects
trim,Views-method	Views objects

-- U --

union,IRanges,IRanges-method	Set operations on IRanges objects
union,RangesList,RangesList-method	RangesList utility functions
unique,Ranges-method	Ranges comparison
unique,Rle-method	Rle objects
universe	List of Ranges
universe,RangedData-method	Data on ranges
universe,RangesList-method	List of Ranges
universe<-	List of Ranges
universe<-,RangedData-method	Data on ranges
universe<-,RangesList-method	List of Ranges
unlist,CompressedList-method	Simple and Compressed List Classes
unlist,IRangesList-method	List of IRanges
unlist,RangedDataList-method	Lists of RangedData
unlist,Ranges-method	Ranges objects
unlist,SimpleList-method	Simple and Compressed List Classes
update,IRanges-method	IRanges and NormalIRanges objects
update,Ranges-method	Ranges objects
updateObject	Update an IRanges object from BioC 2.4 to current version
updateObject,AnnotatedList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,ANY-method	Update an IRanges object from BioC 2.4 to current version
updateObject,CharacterList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,ComplexList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,FilterRules-method	Update an IRanges object from BioC 2.4 to current version
updateObject,IntegerList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,IntervalTree-method	Update an IRanges object from BioC 2.4 to current version
updateObject,IRanges-method	Update an IRanges object from BioC 2.4 to current version
updateObject,IRangesList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,LogicalList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,MaskCollection-method	Update an IRanges object from BioC 2.4 to current version
updateObject,NormalIRanges-method	Update an IRanges object from BioC 2.4 to current version
updateObject,NumericList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RangedData-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RangedDataList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RangesList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RangesMatchingList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RawList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RDApplyParams-method	Update an IRanges object from BioC 2.4 to current version
updateObject,Rle-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RleList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,RleViews-method	Update an IRanges object from BioC 2.4 to current version
updateObject,SplitXDataFrameList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,XDataFrame-method	Update an IRanges object from BioC 2.4 to current version
updateObject,XDataFrameList-method	Update an IRanges object from BioC 2.4 to current version
updateObject,XIntegerViews-method	Update an IRanges object from BioC 2.4 to current version
updateObject,XVector-method	Update an IRanges object from BioC 2.4 to current version

-- V --

values	Data on ranges
values,RangedData-method	Data on ranges
values<-	Data on ranges
values<-,RangedData-method	Data on ranges
var,Rle,missing-method	Rle objects
var,Rle,Rle-method	Rle objects
viewApply	Utility functions and numeric summary of Views of numerics
viewApply,RleViews-method	Utility functions and numeric summary of Views of numerics
viewApply,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewApply,Views-method	Utility functions and numeric summary of Views of numerics
viewMaxs	Utility functions and numeric summary of Views of numerics
viewMaxs,RleViews-method	Utility functions and numeric summary of Views of numerics
viewMaxs,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewMaxs,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
viewMeans	Utility functions and numeric summary of Views of numerics
viewMeans,RleViews-method	Utility functions and numeric summary of Views of numerics
viewMeans,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewMeans,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
viewMins	Utility functions and numeric summary of Views of numerics
viewMins,RleViews-method	Utility functions and numeric summary of Views of numerics
viewMins,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewMins,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
viewRangeMaxs	Utility functions and numeric summary of Views of numerics
viewRangeMaxs,RleViews-method	Utility functions and numeric summary of Views of numerics
viewRangeMaxs,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewRangeMins	Utility functions and numeric summary of Views of numerics
viewRangeMins,RleViews-method	Utility functions and numeric summary of Views of numerics
viewRangeMins,RleViewsList-method	Utility functions and numeric summary of Views of numerics
Views	Views objects
views	Views objects
Views,integer-method	The XIntegerViews class
Views,Rle-method	The RleViews class
Views,RleList-method	List of RleViews
Views,XInteger-method	The XIntegerViews class
Views-class	Views objects
Views-utils	Utility functions and numeric summary of Views of numerics
viewSums	Utility functions and numeric summary of Views of numerics
viewSums,RleViews-method	Utility functions and numeric summary of Views of numerics
viewSums,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewSums,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
viewWhichMaxs	Utility functions and numeric summary of Views of numerics
viewWhichMaxs,RleViews-method	Utility functions and numeric summary of Views of numerics
viewWhichMaxs,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewWhichMaxs,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
viewWhichMins	Utility functions and numeric summary of Views of numerics
viewWhichMins,RleViews-method	Utility functions and numeric summary of Views of numerics
viewWhichMins,RleViewsList-method	Utility functions and numeric summary of Views of numerics
viewWhichMins,XIntegerViews-method	Utility functions and numeric summary of Views of numerics
vmembers	Grouping objects
vmembers,Grouping-method	Grouping objects
vmembers,H2LGrouping-method	Grouping objects

-- W --

which,Rle-method	Rle objects
whichAsIRanges	IRanges utility functions
whichFirstNotNormal	Ranges objects
whichFirstNotNormal,Ranges-method	Ranges objects
width	Ranges objects
width,CompressedIRangesList-method	List of Ranges
width,IRanges-method	IRanges and NormalIRanges objects
width,MaskCollection-method	MaskCollection objects
width,PartitioningByEnd-method	Grouping objects
width,PartitioningByWidth-method	Grouping objects
width,RangedData-method	Data on ranges
width,Ranges-method	Ranges objects
width,RangesList-method	List of Ranges
width,Rle-method	Rle objects
width,XVectorList-method	XVectorList objects
width<-	Ranges objects
width<-,IRanges-method	IRanges and NormalIRanges objects
width<-,RangedData-method	Data on ranges
width<-,RangesList-method	List of Ranges
window,DataTable-method	DataTable objects
window,GroupedIRanges-method	XVectorList objects
window,IRanges-method	IRanges and NormalIRanges objects
window,Rle-method	Rle objects
window,Sequence-method	Sequence objects
window,vector-method	Sequence objects
window,XVector-method	XVector objects
window,XVectorList-method	XVectorList objects
window<-,DataTable-method	DataTable objects
window<-,RangedData-method	Data on ranges
window<-,Sequence-method	Sequence objects
window<-,vector-method	Sequence objects
with,Sequence-method	Sequence objects

-- X --

XDataFrame	External Data Frame
XDouble	XVector objects
XDouble-class	XVector objects
XInteger	XVector objects
XInteger-class	XVector objects
XIntegerViews	The XIntegerViews class
XIntegerViews-class	The XIntegerViews class
XNumeric	XVector objects
XRaw	XVector objects
XRaw-class	XVector objects
XRawList	XVectorList objects
XRawList-class	XVectorList objects
xtabs,ANY,DataTable,ANY,missing-method	Statistical modeling with DataTable
xtabs,ANY,DataTable-method	Statistical modeling with DataTable
XVector	XVector objects
XVector-class	XVector objects
XVectorList	XVectorList objects
XVectorList-class	XVectorList objects

-- misc --

[,CompressedIRangesList-method	List of Ranges
[,CompressedList-method	Simple and Compressed List Classes
[,CompressedSplitDataFrameList-method	List of DataFrames
[,DataFrame-method	External Data Frame
[,FilterRules-method	Collection of Filter Rules
[,GroupedIRanges-method	XVectorList objects
[,IRanges-method	IRanges and NormalIRanges objects
[,MaskCollection-method	MaskCollection objects
[,RangedData-method	Data on ranges
[,Ranges-method	Ranges objects
[,RangesList-method	List of Ranges
[,Rle-method	Rle objects
[,Sequence-method	Sequence objects
[,SimpleIRangesList-method	List of Ranges
[,SimpleList-method	Simple and Compressed List Classes
[,SimpleRangesList-method	List of Ranges
[,SimpleSplitDataFrameList-method	List of DataFrames
[,XDouble-method	XVector objects
[,XInteger-method	XVector objects
[,XRaw-method	XVector objects
[,XVectorList-method	XVectorList objects
[<-,CompressedSplitDataFrameList-method	List of DataFrames
[<-,DataFrame-method	External Data Frame
[<-,RangedData-method	Data on ranges
[<-,Sequence-method	Sequence objects
[<-,SimpleSplitDataFrameList-method	List of DataFrames
[[,Binning-method	Grouping objects
[[,CompressedList-method	Simple and Compressed List Classes
[[,DataFrame-method	External Data Frame
[[,H2LGrouping-method	Grouping objects
[[,MaskCollection-method	MaskCollection objects
[[,Partitioning-method	Grouping objects
[[,RangedData-method	Data on ranges
[[,Ranges-method	Ranges objects
[[,Sequence-method	Sequence objects
[[,SimpleList-method	Simple and Compressed List Classes
[[,Views-method	Views objects
[[,XVectorList-method	XVectorList objects
[[<-,CompressedList-method	Simple and Compressed List Classes
[[<-,DataFrame-method	External Data Frame
[[<-,FilterRules-method	Collection of Filter Rules
[[<-,RangedData-method	Data on ranges
[[<-,SimpleList-method	Simple and Compressed List Classes