Infrastructure for manipulating intervals on sequences

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Documentation for package ‘IRanges’ version 1.1.55

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A C D E F G I L M N O P Q R S T U V W X misc

!,Rle-method Rle objects
!= Ranges comparison
!=,integer,XIntegerViews-method The XIntegerViews class
!=,integer,XRleIntegerViews-method The XRleIntegerViews 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
!=,XRleInteger,XRleIntegerViews-method The XRleIntegerViews class
!=,XRleIntegerViews,integer-method The XRleIntegerViews class
!=,XRleIntegerViews,XRleInteger-method The XRleIntegerViews class
!=,XRleIntegerViews,XRleIntegerViews-method The XRleIntegerViews class
$,RangedData-method Data on ranges
$,TypedList-method Typed Lists
$<-,RangedData-method Data on ranges
$<-,TypedList-method Typed Lists
%in%,Ranges,Ranges-method Interval Search Trees
%in%,Rle,ANY-method Rle objects
*,Ranges,numeric-method IRanges utility functions
< Ranges comparison
<,Ranges,Ranges-method Ranges comparison
<= Ranges comparison
<=,Ranges,Ranges-method Ranges comparison
== Ranges comparison
==,integer,XIntegerViews-method The XIntegerViews class
==,integer,XRleIntegerViews-method The XRleIntegerViews class
==,Ranges,Ranges-method Ranges comparison
==,XInteger,XInteger-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
==,XNumeric,XNumeric-method Sequence objects
==,XRle,XRle-method Sequence objects
==,XRleInteger,XRleIntegerViews-method The XRleIntegerViews class
==,XRleIntegerViews,integer-method The XRleIntegerViews class
==,XRleIntegerViews,XRleInteger-method The XRleIntegerViews class
==,XRleIntegerViews,XRleIntegerViews-method The XRleIntegerViews 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<-,FilterRules-method Collection of Filter Rules
active<-,MaskCollection-method MaskCollection objects
aggregate,Rle-method Rle objects
AnnotatedList Annotated Lists
AnnotatedList-class Annotated Lists
append,FilterRules,FilterRules-method Collection of Filter Rules
append,MaskCollection,MaskCollection-method MaskCollection objects
append,TypedList,TypedList-method Typed Lists
applyFun Applying over spaces
applyFun,RDApplyParams-method Applying over spaces
applyFun<-,RDApplyParams-method Applying over spaces
applyParams Applying over spaces
applyParams,RDApplyParams-method Applying over spaces
applyParams<-,RDApplyParams-method Applying over spaces
Arith,integer,XRleInteger-method Sequence objects
Arith,XRleInteger,integer-method Sequence objects
Arith,XRleInteger,XRleInteger-method Sequence objects
as.character,Rle-method Rle objects
as.complex,Rle-method Rle 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,SplitXDataFrameList-method List of XDataFrames
as.data.frame,XDataFrame-method External Data Frame
as.factor,Rle-method Rle objects
as.integer,Rle-method Rle objects
as.integer,XInteger-method Sequence objects
as.integer,XIntegerViews-method The XIntegerViews class
as.integer,XRaw-method Sequence objects
as.integer,XRleInteger-method Sequence objects
as.integer,XRleIntegerViews-method The XRleIntegerViews class
as.list,TypedList-method Typed Lists
as.list,XDataFrame-method External Data Frame
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,Rle-method Rle objects
as.numeric,XNumeric-method Sequence objects
as.numeric,XSequence-method Sequence objects
as.raw,Rle-method Rle objects
as.table,RangesMatching-method Matchings between Ranges
as.table,RangesMatchingList-method List of Matchings between Ranges
as.vector,Rle,missing-method Rle objects
as.vector,XInteger,missing-method Sequence objects
as.vector,XNumeric,missing-method Sequence objects
as.vector,XRleInteger,missing-method Sequence objects
asNormalIRanges IRanges utility functions

-- C --

c,FilterRules-method Collection of Filter Rules
c,IRanges-method IRanges and NormalIRanges objects
c,RangedData-method Data on ranges
c,Rle-method Rle objects
c,TypedList-method Typed Lists
c,XRaw-method Sequence objects
cbind External Data Frame
cbind,XDataFrame-method External Data Frame
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:IRanges IRanges and NormalIRanges objects
class:MaskCollection MaskCollection objects
class:NormalIRanges IRanges and NormalIRanges objects
class:Ranges Ranges objects
class:Rle Rle objects
class:RleViews The RleViews class
class:Sequence Sequence objects
class:Views Views objects
class:XInteger Sequence objects
class:XIntegerViews The XIntegerViews class
class:XNumeric Sequence objects
class:XRaw Sequence objects
class:XRle Sequence objects
class:XRleInteger Sequence objects
class:XRleIntegerViews The XRleIntegerViews class
class:XSequence Sequence objects
coerce,ANY,XDataFrame-method External Data Frame
coerce,data.frame,XDataFrame-method External Data Frame
coerce,factor,Rle-method Rle objects
coerce,integer,XDataFrame-method External Data Frame
coerce,integer,XInteger-method Sequence objects
coerce,integer,XRleInteger-method Sequence objects
coerce,integer,XSequence-method Sequence 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,XDataFrame-method External Data Frame
coerce,MaskCollection,NormalIRanges-method MaskCollection objects
coerce,matrix,XDataFrame-method External Data Frame
coerce,numeric,XNumeric-method Sequence objects
coerce,numeric,XSequence-method Sequence objects
coerce,RangedData,XDataFrame-method Data on ranges
coerce,Ranges,IntervalTree-method Interval Search Trees
coerce,RangesList,IRangesList-method List of Ranges
coerce,RangesList,RangedData-method List of Ranges
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,numeric-method Rle objects
coerce,Rle,RangedData-method Data on ranges
coerce,Rle,raw-method Rle objects
coerce,Rle,vector-method Rle objects
coerce,SplitXDataFrameList,XDataFrame-method List of XDataFrames
coerce,TypedList,list-method Typed Lists
coerce,vector,Rle-method Rle objects
coerce,Views,NormalIRanges-method Views objects
coerce,XDataFrame,data.frame-method External Data Frame
coerce,XRle,RangedData-method Data on ranges
Complex,Rle-method Rle objects
ComplexList Lists of Atomic Vectors in Natural and Rle Form
ComplexList-class Lists of Atomic Vectors in Natural and Rle Form
cor,Rle,Rle-method Rle objects
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

-- D --

desc MaskCollection objects
desc,MaskCollection-method MaskCollection objects
desc<-,MaskCollection-method MaskCollection objects
diff,Rle-method Rle objects
dim,RangedData-method Data on ranges
dim,RangesMatching-method Matchings between Ranges
dim,XDataFrame-method External Data Frame
dim,XDataFrameList-method List of XDataFrames
dimnames,RangedData-method Data on ranges
dimnames,XDataFrame-method External Data Frame
dimnames,XDataFrameList-method List of XDataFrames
dimnames<-,RangedData-method Data on ranges
dimnames<-,XDataFrame-method External Data Frame
disjoin Making Ranges disjoint
disjoin,Ranges-method Making Ranges disjoint
disjointBins Making Ranges disjoint
disjointBins,Ranges-method Making Ranges disjoint
duplicated Ranges comparison
duplicated,Ranges-method Ranges comparison

-- E --

elementClass Typed Lists
elementClass,TypedList-method Typed Lists
elementLengths Typed Lists
elementLengths,TypedList-method Typed Lists
elementMetadata Annotated Lists
elementMetadata,AnnotatedList-method Annotated Lists
elementMetadata<-,AnnotatedList,XDataFrameORNULL-method Annotated Lists
end,RangedData-method Data on ranges
end,Ranges-method Ranges objects
end,RangesList-method List of Ranges
end,Rle-method Rle objects
end,XRanges-method External Ranges
end<-,IRanges-method IRanges and NormalIRanges objects
eval,expressionORlanguage,RangedData-method RangedData utility functions
eval,expressionORlanguage,XDataFrame-method XDataFrame utility functions
eval,FilterRules,ANY-method Collection of Filter Rules

-- F --

FilterRules Collection of Filter Rules
filterRules Applying over spaces
filterRules,RDApplyParams-method Applying over spaces
FilterRules-class Collection of Filter Rules
filterRules<-,RDApplyParams-method Applying over spaces
findRange Rle objects
findRange,Rle-method Rle objects
first Ranges objects
first,Ranges-method Ranges objects
flank IRanges utility functions
flank,Ranges-method IRanges utility functions
follow Nearest neighbor finding
follow,Ranges,RangesORmissing-method Nearest neighbor finding

-- G --

gaps IRanges utility functions
gaps,IRanges-method IRanges utility functions
gaps,MaskCollection-method MaskCollection objects
gaps,RangesList-method RangesList utility functions
gaps,Views-method Views objects
gaps,XRanges-method External Ranges
gsub,ANY,ANY,Rle-method Rle 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
IntervalTree Interval Search Trees
IntervalTree-class Interval Search Trees
intToAdjacentRanges IRanges utility functions
intToRanges IRanges utility functions
IRanges IRanges and NormalIRanges objects
IRanges-class IRanges and NormalIRanges objects
IRanges-setops Set operations on IRanges objects
IRanges-utils IRanges utility functions
IRangesList List of IRanges
IRangesList-class List of IRanges
is.array,XDataFrame-method External Data Frame
is.na,Rle-method Rle objects
isDisjoint Ranges objects
isDisjoint,Ranges-method Ranges objects
isEmpty Ranges objects
isEmpty,MaskCollection-method MaskCollection objects
isEmpty,NormalIRanges-method IRanges and NormalIRanges objects
isEmpty,Ranges-method Ranges objects
isEmpty,TypedList-method Typed Lists
isNormal Ranges objects
isNormal,Ranges-method Ranges objects

-- L --

lapply,RangedData,ANY-method Data on ranges
lapply,TypedList,character-method Typed Lists
lapply,TypedList,function-method Typed Lists
last Ranges objects
last,Ranges-method Ranges objects
length,IntervalTree-method Interval Search Trees
length,MaskCollection-method MaskCollection objects
length,RangedData-method Data on ranges
length,Ranges-method Ranges objects
length,Rle-method Rle objects
length,TypedList-method Typed Lists
length,XRle-method Sequence objects
length,XSequence-method Sequence objects
LogicalList Lists of Atomic Vectors in Natural and Rle Form
LogicalList-class Lists of Atomic Vectors in Natural and Rle Form

-- M --

mad,Rle-method Rle 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
matchMatrix Matchings between Ranges
matchMatrix,RangesMatching-method Matchings between Ranges
Math,Rle-method Rle objects
Math2,Rle-method Rle objects
max,MaskCollection-method MaskCollection objects
max,NormalIRanges-method IRanges and NormalIRanges objects
mean,Rle-method Rle objects
median,Rle-method Rle objects
metadata Annotated Lists
metadata,AnnotatedList-method Annotated Lists
metadata<-,AnnotatedList,list-method Annotated Lists
mid Ranges objects
mid,Ranges-method Ranges objects
min,MaskCollection-method MaskCollection objects
min,NormalIRanges-method IRanges and NormalIRanges objects

-- N --

names,IRanges-method IRanges and NormalIRanges objects
names,MaskCollection-method MaskCollection objects
names,RangedData-method Data on ranges
names,TypedList-method Typed Lists
names<-,IRanges-method IRanges and NormalIRanges objects
names<-,MaskCollection-method MaskCollection objects
names<-,RangedData-method Data on ranges
names<-,TypedList-method Typed Lists
narrow IRanges utility functions
narrow,IRanges-method IRanges utility functions
narrow,NormalIRanges-method IRanges utility functions
narrow,Views-method Views objects
nchar,Rle-method Rle objects
nearest Nearest neighbor finding
nearest,Ranges,RangesORmissing-method Nearest neighbor finding
newViews Views objects
nir_list MaskCollection objects
nir_list,MaskCollection-method MaskCollection objects
NormalIRanges IRanges and NormalIRanges objects
NormalIRanges-class IRanges and NormalIRanges objects
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,RangesList,ANY-method List of Ranges
Ops,Rle,Rle-method Rle objects
Ops,Rle,vector-method Rle objects
Ops,vector,Rle-method Rle objects
order Ranges comparison
order,Ranges-method Ranges comparison
overlap Interval Search Trees
overlap,IntervalTree,Ranges-method Interval Search Trees
overlap,Ranges,integer-method Interval Search Trees
overlap,Ranges,missing-method Interval Search Trees
overlap,Ranges,Ranges-method Interval Search Trees
overlap,RangesList,RangesList-method Interval Search Trees

-- P --

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
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

-- 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<-,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
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 comparison
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 External Data Frame
rbind,RangedData-method Data on ranges
rbind,XDataFrame-method External Data Frame
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,IRanges-method IRanges utility functions
reduce,MaskCollection-method MaskCollection objects
reduce,RangesList-method RangesList utility functions
reduce,XRanges-method External Ranges
reducerFun Applying over spaces
reducerFun,RDApplyParams-method Applying over spaces
reducerFun<-,RDApplyParams-method Applying over spaces
reducerParams Applying over spaces
reducerParams,RDApplyParams-method Applying over spaces
reducerParams<-,RDApplyParams-method Applying over spaces
reflect IRanges utility functions
reflect,Ranges-method IRanges utility functions
rep,Ranges-method Ranges objects
rep,Rle-method Rle objects
rep,Sequence-method Sequence objects
rep,XRle-method Sequence objects
rep.int Rle objects
rep.int,Rle-method Rle objects
restrict IRanges utility functions
restrict,IRanges-method IRanges utility functions
restrict,Views-method Views objects
rev,Rle-method Rle objects
reverse Reverse ranges
reverse,IRanges-method Reverse ranges
reverse,MaskCollection-method Reverse ranges
reverse,NormalIRanges-method Reverse ranges
reverse,XRle-method Sequence objects
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
runLength Rle objects
runLength,Rle-method Rle objects
runLength<-,Rle-method Rle objects
runValue Rle objects
runValue,Rle-method Rle objects
runValue<-,Rle-method Rle objects

-- S --

score Alignments between sequences
score,AlignmentSpace-method Alignments between sequences
sd,Rle-method Rle objects
Sequence Sequence objects
Sequence-class Sequence objects
setdiff,IRanges,IRanges-method Set operations on IRanges objects
shift IRanges utility functions
shift,IRanges-method IRanges utility functions
shiftApply Rle objects
shiftApply,Rle,Rle-method Rle objects
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,RleViews-method The RleViews class
show,TypedList-method Typed Lists
show,XDataFrame-method External Data Frame
show,XIntegerViews-method The XIntegerViews class
show,XNumeric-method Sequence objects
show,XRleInteger-method Sequence objects
show,XRleIntegerViews-method The XRleIntegerViews class
show,XSequence-method Sequence objects
simplify Applying over spaces
simplify,RDApplyParams-method 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,XInteger-method Utility functions and numeric summary of Views of numerics
slice,XRleInteger-method Utility functions and numeric summary of Views of numerics
solveUserSEW The SEW (Start/End/Width) interface
sort Ranges comparison
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,RangedData-method Data on ranges
split,Ranges-method List of Ranges
split,XDataFrame-method External Data Frame
SplitXDataFrameList List of XDataFrames
SplitXDataFrameList-class List of XDataFrames
start,IRanges-method IRanges and NormalIRanges objects
start,RangedData-method Data on ranges
start,Ranges-method Ranges objects
start,RangesList-method List of Ranges
start,Rle-method Rle objects
start,XRanges-method External Ranges
start<-,IRanges-method IRanges and NormalIRanges objects
sub,ANY,ANY,Rle-method Rle objects
subject Views objects
subject,Views-method Views objects
subseq Sequence objects
subseq,MaskCollection-method MaskCollection objects
subseq,Rle-method Rle objects
subseq,Sequence-method Sequence objects
subseq,vector-method Sequence objects
subseq,XRle-method Sequence objects
subseq,XSequence-method Sequence objects
subseq<-,ANY-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,IRangesList-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
threebands IRanges utility functions
threebands,IRanges-method IRanges utility functions
tolower,Rle-method Rle objects
toNormalIRanges IRanges utility functions
toupper,Rle-method Rle objects
trim Views objects
trim,Views-method Views objects
TypedList-class Typed Lists

-- U --

union,IRanges,IRanges-method Set operations on IRanges objects
unique Ranges comparison
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<-,RangedData-method Data on ranges
universe<-,RangesList-method List of Ranges
unlist,IRangesList-method List of IRanges
unlist,RangedDataList-method Lists of RangedData
unlist,TypedList-method Typed Lists
update,IRanges-method IRanges and NormalIRanges objects
updateRangedData Data on ranges
updateTypedList Typed Lists

-- V --

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,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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewMaxs,XRleIntegerViews-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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewMins,XRleIntegerViews-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
viewRangeMins Utility functions and numeric summary of Views of numerics
viewRangeMins,RleViews-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,XInteger-method The XIntegerViews class
Views,XRleInteger-method The XRleIntegerViews 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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewSums,XRleIntegerViews-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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewWhichMaxs,XRleIntegerViews-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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewWhichMins,XRleIntegerViews-method Utility functions and numeric summary of Views of numerics

-- W --

which,Rle-method Rle objects
whichAsIRanges IRanges utility functions
whichFirstNotNormal Ranges objects
whichFirstNotNormal,Ranges-method Ranges objects
width Ranges objects
width,IRanges-method IRanges and NormalIRanges objects
width,MaskCollection-method MaskCollection objects
width,RangedData-method Data on ranges
width,Ranges-method Ranges objects
width,RangesList-method List of Ranges
width,Rle-method Rle objects
width,XRanges-method External Ranges
width<-,IRanges-method IRanges and NormalIRanges objects
window,Rle-method Rle objects

-- X --

XDataFrame External Data Frame
XDataFrame-class External Data Frame
XDataFrame-utils XDataFrame utility functions
XDataFrameList List of XDataFrames
XDataFrameList-class List of XDataFrames
XInteger Sequence objects
XInteger-class Sequence objects
XIntegerViews The XIntegerViews class
XIntegerViews-class The XIntegerViews class
XNumeric Sequence objects
XNumeric-class Sequence objects
XRanges External Ranges
XRanges-class External Ranges
XRaw Sequence objects
XRaw-class Sequence objects
XRle Sequence objects
XRle-class Sequence objects
XRleInteger Sequence objects
XRleInteger-class Sequence objects
XRleIntegerViews The XRleIntegerViews class
XRleIntegerViews-class The XRleIntegerViews class
XSequence Sequence objects
XSequence-class Sequence objects

-- misc --

[,FilterRules-method Collection of Filter Rules
[,IRanges-method IRanges and NormalIRanges objects
[,MaskCollection-method MaskCollection objects
[,RangedData-method Data on ranges
[,RangesList-method List of Ranges
[,Rle-method Rle objects
[,TypedList-method Typed Lists
[,XDataFrame-method External Data Frame
[,XInteger-method Sequence objects
[,XNumeric-method Sequence objects
[,XRaw-method Sequence objects
[,XRle-method Sequence objects
[<-,MaskCollection-method MaskCollection objects
[<-,RangedData-method Data on ranges
[<-,Ranges-method Ranges objects
[<-,Sequence-method Sequence objects
[<-,TypedList-method Typed Lists
[[,MaskCollection-method MaskCollection objects
[[,RangedData-method Data on ranges
[[,TypedList-method Typed Lists
[[,Views-method Views objects
[[,XDataFrame-method External Data Frame
[[,XIntegerViews-method The XIntegerViews class
[[,XRleIntegerViews-method The XRleIntegerViews class
[[<-,FilterRules-method Collection of Filter Rules
[[<-,MaskCollection-method MaskCollection objects
[[<-,RangedData-method Data on ranges
[[<-,TypedList-method Typed Lists
[[<-,Views-method Views objects
[[<-,XDataFrame-method External Data Frame
[[<-,XIntegerViews-method The XIntegerViews class
[[<-,XRleIntegerViews-method The XRleIntegerViews class