Low-level containers for storing sets of integer ranges

[Package List] [Top]

Documentation for package ‘IRanges’ version 1.0.16

Help Pages

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

!=,integer,XIntegerViews-method The XIntegerViews class
!=,integer,XRleIntegerViews-method The XRleIntegerViews class
!=,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
%in%,Ranges,Ranges-method Interval Search Trees
==,integer,XIntegerViews-method The XIntegerViews class
==,integer,XRleIntegerViews-method The XRleIntegerViews class
==,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

-- 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
annotation Data on ranges
annotation,RangedData-method Data on ranges
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.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,SplitXDataFrame-method Split XDataFrame
as.data.frame,XDataFrame-method External Data Frame
as.integer,XInteger-method Sequence objects
as.integer,XIntegerViews-method The XIntegerViews class
as.integer,XRleInteger-method Sequence objects
as.integer,XRleIntegerViews-method The XRleIntegerViews class
as.list,TypedList-method Typed Lists
as.matrix,Ranges-method Ranges objects
as.matrix,RangesMatching-method Matchings between Ranges
as.numeric,XNumeric-method Sequence objects
as.table,RangesMatching-method Matchings between Ranges
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,GenomicData-method Data on a Genome
c,IRanges-method IRanges and NormalIRanges objects
c,RangedData-method Data on ranges
c,TypedList-method Typed Lists
cbind External Data Frame
cbind,XDataFrame-method External Data Frame
chrom Data on a Genome
chrom,GenomicData-method Data on a Genome
class:IRanges IRanges and NormalIRanges objects
class:MaskCollection MaskCollection objects
class:NormalIRanges IRanges and NormalIRanges objects
class:Ranges Ranges objects
class:Sequence Sequence objects
class:SequenceORvector 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,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,NormalIRanges-method List of IRanges
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,SplitXDataFrame,XDataFrame-method Split XDataFrame
coerce,TypedList,list-method Typed Lists
coerce,Views,NormalIRanges-method Views objects
coerce,XDataFrame,data.frame-method External Data Frame
coerce,XRle,GenomicData-method Data on a Genome
coerce,XRle,RangedData-method Data on ranges
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
dim,RangedData-method Data on ranges
dim,SplitXDataFrame-method Split XDataFrame
dim,XDataFrame-method External Data Frame
dimnames,RangedData-method Data on ranges
dimnames,SplitXDataFrame-method Split XDataFrame
dimnames,XDataFrame-method External Data Frame
dimnames<-,XDataFrame,ANY-method External Data Frame
duplicated,Ranges-method Ranges objects

-- E --

elementClass Typed Lists
elementClass,TypedList-method Typed Lists
elements Typed Lists
elements,TypedList-method Typed Lists
end,RangedData-method Data on ranges
end,Ranges-method Ranges objects
end,RangesList-method List of Ranges
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
first Ranges objects
first,Ranges-method Ranges objects

-- 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
genome Data on a Genome
genome,GenomicData-method Data on a Genome
GenomicData Data on a Genome
GenomicData-class Data on a Genome

-- I --

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
isEmpty Ranges objects
isEmpty,MaskCollection-method MaskCollection objects
isEmpty,NormalIRanges-method IRanges and NormalIRanges objects
isEmpty,Ranges-method Ranges objects
isEmpty,RangesList-method List of Ranges
isNormal Ranges objects
isNormal,Ranges-method Ranges objects

-- L --

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,TypedList-method Typed Lists
length,XRle-method Sequence objects
length,XSequence-method Sequence objects

-- M --

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
max,MaskCollection-method MaskCollection objects
max,NormalIRanges-method IRanges and NormalIRanges 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
newViews Views objects
nir_list MaskCollection objects
nir_list,MaskCollection-method MaskCollection objects
NormalIRanges IRanges and NormalIRanges objects
NormalIRanges-class IRanges and NormalIRanges objects

-- O --

overlap Interval Search Trees
overlap,IntervalTree,Ranges-method Interval Search Trees
overlap,Ranges,missing-method Interval Search Trees
overlap,Ranges,Ranges-method Interval Search Trees

-- P --

pintersect Set operations on IRanges objects
pintersect,IRanges,IRanges-method Set operations on IRanges objects
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

-- R --

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-class Ranges objects
RangesList List of Ranges
RangesList-class List of Ranges
RangesList-utils RangesList utility functions
RangesMatching-class Matchings between Ranges
rbind External Data Frame
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
rep,Ranges-method Ranges objects
rep,Sequence-method Sequence objects
rep,XRle-method Sequence objects
restrict IRanges utility functions
restrict,IRanges-method IRanges utility functions
restrict,Views-method Views objects
reverse Reverse ranges
reverse,IRanges-method Reverse ranges
reverse,MaskCollection-method Reverse ranges
reverse,NormalIRanges-method Reverse ranges
reverse,XRle-method Sequence objects

-- S --

Sequence Sequence objects
Sequence-class Sequence objects
SequenceORvector Sequence objects
SequenceORvector-class Sequence objects
setdiff,IRanges,IRanges-method Set operations on IRanges objects
shift IRanges utility functions
shift,IRanges-method IRanges utility functions
show,MaskCollection-method MaskCollection objects
show,RangedData-method Data on ranges
show,Ranges-method Ranges objects
show,RangesList-method List of Ranges
show,TypedList-method Typed Lists
show,XDataFrame-method External Data Frame
show,XInteger-method Sequence objects
show,XIntegerViews-method The XIntegerViews class
show,XNumeric-method Sequence objects
show,XRleInteger-method Sequence objects
show,XRleIntegerViews-method The XRleIntegerViews class
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,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
split,RangedData-method Data on ranges
split,Ranges-method List of Ranges
split,XDataFrame-method External Data Frame
SplitXDataFrame Split XDataFrame
SplitXDataFrame-class Split XDataFrame
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,XRanges-method External Ranges
start<-,IRanges-method IRanges and NormalIRanges objects
strand Data on a Genome
strand,GenomicData-method Data on a Genome
strand,missing-method Data on a Genome
subject Views objects
subject,Views-method Views objects
subseq Sequence objects
subseq,MaskCollection-method MaskCollection objects
subseq,SequenceORvector-method Sequence objects
subseq,XSequence-method Sequence objects
subviews Views objects
subviews,Views-method Views objects
successiveIRanges IRanges utility functions
successiveViews Views objects
summary,RangesList-method List of Ranges

-- T --

t,RangesMatching-method Matchings between Ranges
toNormalIRanges IRanges utility functions
trim Views objects
trim,Views-method Views objects
TypedList-class Typed Lists

-- U --

union,IRanges,IRanges-method Set operations on IRanges objects
unlist,IRangesList-method List of IRanges
unlist,SplitXDataFrame-method Split XDataFrame
unlist,TypedList-method Typed Lists
update,IRanges-method IRanges and NormalIRanges objects

-- V --

values Data on ranges
values,RangedData-method Data on ranges
viewMaxs 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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewMins,XRleIntegerViews-method Utility functions and numeric summary of Views of numerics
Views Views objects
views Views objects
Views,integer-method The XIntegerViews 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,XIntegerViews-method Utility functions and numeric summary of Views of numerics
viewSums,XRleIntegerViews-method Utility functions and numeric summary of Views of numerics

-- W --

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,XRanges-method External Ranges
width<-,IRanges-method IRanges and NormalIRanges objects
width<-,Views-method Views objects

-- X --

XDataFrame External Data Frame
XDataFrame-class External Data Frame
XDataFrame-utils XDataFrame utility functions
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,ANY,ANY,ANY-method Collection of Filter Rules
[,IRanges,ANY,ANY,ANY-method IRanges and NormalIRanges objects
[,MaskCollection,ANY,ANY,ANY-method MaskCollection objects
[,RangedData,ANY,ANY,ANY-method Data on ranges
[,TypedList,ANY,ANY,ANY-method Typed Lists
[,XDataFrame,ANY,ANY,ANY-method External Data Frame
[,XInteger,ANY,ANY,ANY-method Sequence objects
[,XNumeric,ANY,ANY,ANY-method Sequence objects
[,XRle,ANY,ANY,ANY-method Sequence objects
[<-,MaskCollection,ANY,ANY,ANY-method MaskCollection objects
[<-,RangedData,ANY,ANY,ANY-method Data on ranges
[<-,Ranges,ANY,ANY,ANY-method Ranges objects
[<-,Sequence,ANY,ANY,ANY-method Sequence objects
[<-,TypedList,ANY,ANY,ANY-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