Infrastructure for manipulating intervals on sequences


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Documentation for package ‘IRanges’ version 1.4.7

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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,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
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<- 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
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