# Infrastructure for manipulating intervals on sequences

## Documentation for package ‘IRanges’ version 2.2.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

## -- A --

active | MaskCollection objects
active-method | Collection of Filter Rules
active-method | MaskCollection objects
active<- | MaskCollection objects
active<--method | Collection of Filter Rules
active<--method | MaskCollection objects
all-method | Lists of Atomic Vectors in Natural and Rle Form
append-method | Collection of Filter Rules
append-method | MaskCollection objects
applyFun | Applying over spaces
applyFun-method | Applying over spaces
applyFun<- | Applying over spaces
applyFun<--method | Applying over spaces
applyParams | Applying over spaces
applyParams-method | Applying over spaces
applyParams<- | Applying over spaces
applyParams<--method | Applying over spaces
as.data.frame-method | GappedRanges objects
as.data.frame-method | Examples of basic manipulation of Hits objects
as.data.frame-method | Data on ranges
as.data.frame-method | Ranges objects
as.data.frame.GappedRanges | GappedRanges objects
as.data.frame.Hits | Examples of basic manipulation of Hits objects
as.data.frame.RangedData | Data on ranges
as.data.frame.Ranges | Ranges objects
as.env-method | List of DataFrames
as.env-method | Data on ranges
as.integer-method | Ranges objects
as.list-method | Lists of Atomic Vectors in Natural and Rle Form
as.list-method | Examples of basic manipulation of Hits objects
as.list-method | List of IRanges and NormalIRanges
as.list-method | Vector objects (old man page)
as.list.CompressedNormalIRangesList | List of IRanges and NormalIRanges
as.list.Hits | Examples of basic manipulation of Hits objects
as.list.Vector | Vector objects (old man page)
as.matrix-method | List of Hits objects
as.matrix-method | Ranges objects
as.matrix-method | Views objects
as.matrix-method | List of Views
as.table-method | List of Hits objects
as.vector-method | Lists of Atomic Vectors in Natural and Rle Form
asNormalIRanges | IRanges utility functions
AtomicList | Lists of Atomic Vectors in Natural and Rle Form
AtomicList-class | Lists of Atomic Vectors in Natural and Rle Form

## -- B --

breakInChunks | IRanges utility functions

## -- C --

c-method | CompressedList objects
c-method | Collection of Filter Rules
c-method | GappedRanges objects
c-method | IRanges and NormalIRanges objects
c-method | Data on ranges
c-method | Views objects
cbind-method | List of DataFrames
cbind-method | Matrix for Filter Results
CharacterList | Lists of Atomic Vectors in Natural and Rle Form
CharacterList-class | Lists of Atomic Vectors in Natural and Rle Form
chartr-method | Lists of Atomic Vectors in Natural and Rle Form
class:AtomicList | Lists of Atomic Vectors in Natural and Rle Form
class:CharacterList | Lists of Atomic Vectors in Natural and Rle Form
class:ComplexList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedAtomicList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedCharacterList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedComplexList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedFactorList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedHitsList | List of Hits objects
class:CompressedIntegerList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedIRangesList | List of IRanges and NormalIRanges
class:CompressedList | CompressedList objects
class:CompressedLogicalList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedNormalIRangesList | List of IRanges and NormalIRanges
class:CompressedNumericList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedRawList | Lists of Atomic Vectors in Natural and Rle Form
class:CompressedRleList | Lists of Atomic Vectors in Natural and Rle Form
class:Dups | Grouping objects
class:FactorList | Lists of Atomic Vectors in Natural and Rle Form
class:GappedRanges | GappedRanges objects
class:Grouping | Grouping objects
class:H2LGrouping | Grouping objects
class:HitsList | List of Hits objects
class:IntegerList | Lists of Atomic Vectors in Natural and Rle Form
class:IRanges | IRanges and NormalIRanges objects
class:IRangesList | List of IRanges and NormalIRanges
class:LogicalList | Lists of Atomic Vectors in Natural and Rle Form
class:ManyToOneGrouping | Grouping objects
class:MaskCollection | MaskCollection objects
class:NCList | Nested Containment List objects
class:NCLists | Nested Containment List objects
class:NormalIRanges | IRanges and NormalIRanges objects
class:NormalIRangesList | List of IRanges and NormalIRanges
class:NumericList | Lists of Atomic Vectors in Natural and Rle Form
class:Partitioning | Grouping objects
class:PartitioningByEnd | Grouping objects
class:PartitioningByWidth | Grouping objects
class:PartitioningMap | Grouping objects
class:RangedData | Data on ranges
class:Ranges | Ranges objects
class:RangesList-class | List of Ranges
class:RangesORmissing | Finding the nearest range neighbor
class:RawList | Lists of Atomic Vectors in Natural and Rle Form
class:RleList | Lists of Atomic Vectors in Natural and Rle Form
class:RleViews | The RleViews class
class:SimpleAtomicList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleCharacterList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleComplexList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleFactorList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleIntegerList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleIRangesList | List of IRanges and NormalIRanges
class:SimpleLogicalList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleNormalIRangesList | List of IRanges and NormalIRanges
class:SimpleNumericList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleRangesList-class | List of Ranges
class:SimpleRawList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleRleList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleViewsList | List of Views
class:Views | Views objects
class:ViewsList | List of Views
classNameForDisplay-method | CompressedList objects
coerce-method | Lists of Atomic Vectors in Natural and Rle Form
coerce-method | CompressedList objects
coerce-method | List of DataFrames
coerce-method | Collection of Filter Rules
coerce-method | GappedRanges objects
coerce-method | Grouping objects
coerce-method | Examples of basic manipulation of Hits objects
coerce-method | IRanges and NormalIRanges objects
coerce-method | IRanges utility functions
coerce-method | List of IRanges and NormalIRanges
coerce-method | Interval Search Forests
coerce-method | Interval Search Trees
coerce-method | MaskCollection objects
coerce-method | Nested Containment List objects
coerce-method | Data on ranges
coerce-method | Selection of ranges and columns
coerce-method | List of Ranges
coerce-method | Rle objects (old man page)
coerce-method | The RleViews class
coerce-method | List of RleViews
coerce-method | Views objects
collapse | MaskCollection objects
collapse-method | MaskCollection objects
colnames-method | List of DataFrames
colnames-method | Data on ranges
colnames-method | Selection of ranges and columns
colnames<--method | List of DataFrames
colnames<--method | Data on ranges
colnames<--method | Selection of ranges and columns
columnMetadata | List of DataFrames
columnMetadata-method | List of DataFrames
columnMetadata-method | Data on ranges
columnMetadata<- | List of DataFrames
columnMetadata<--method | List of DataFrames
columnMetadata<--method | Data on ranges
compare | Comparing and ordering ranges
compare-method | Comparing and ordering ranges
Complex-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 | 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
CompressedFactorList | Lists of Atomic Vectors in Natural and Rle Form
CompressedFactorList-class | Lists of Atomic Vectors in Natural and Rle Form
CompressedHitsList | List of Hits objects
CompressedHitsList-class | List of Hits objects
CompressedIntegerList | Lists of Atomic Vectors in Natural and Rle Form
CompressedIntegerList-class | Lists of Atomic Vectors in Natural and Rle Form
CompressedIRangesList | List of IRanges and NormalIRanges
CompressedIRangesList-class | List of IRanges and NormalIRanges
CompressedList | CompressedList objects
CompressedList-class | CompressedList objects
CompressedLogicalList | Lists of Atomic Vectors in Natural and Rle Form
CompressedLogicalList-class | Lists of Atomic Vectors in Natural and Rle Form
CompressedNormalIRangesList | List of IRanges and NormalIRanges
CompressedNormalIRangesList-class | List of IRanges and NormalIRanges
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-method | Lists of Atomic Vectors in Natural and Rle Form
countOverlaps | Finding overlapping ranges
countOverlaps-method | Finding overlapping ranges
cov-method | Lists of Atomic Vectors in Natural and Rle Form
coverage | Coverage of a set of ranges
coverage-method | Coverage of a set of ranges
coverage-methods | Coverage of a set of ranges
cummax-method | Lists of Atomic Vectors in Natural and Rle Form
cummin-method | Lists of Atomic Vectors in Natural and Rle Form
cumprod-method | Lists of Atomic Vectors in Natural and Rle Form
cumsum-method | Lists of Atomic Vectors in Natural and Rle Form

## -- D --

DataFrame-utils | Common operations on DataFrame objects
DataFrameList | List of DataFrames
DataFrameList-class | List of DataFrames
desc | MaskCollection objects
desc-method | MaskCollection objects
desc<- | MaskCollection objects
desc<--method | MaskCollection objects
diff-method | Lists of Atomic Vectors in Natural and Rle Form
dim-method | List of DataFrames
dimnames-method | List of DataFrames
dimnames<--method | List of DataFrames
disjoin | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjoin-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjointBins | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjointBins-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
distance | Finding the nearest range neighbor
distance-method | Finding the nearest range neighbor
distanceToNearest | Finding the nearest range neighbor
distanceToNearest-method | Finding the nearest range neighbor
drop-method | Lists of Atomic Vectors in Natural and Rle Form
duplicated-method | Lists of Atomic Vectors in Natural and Rle Form
duplicated-method | Grouping objects
duplicated.CompressedIntegerList | Lists of Atomic Vectors in Natural and Rle Form
duplicated.CompressedList | Lists of Atomic Vectors in Natural and Rle Form
duplicated.Dups | Grouping objects
Dups | Grouping objects
Dups-class | Grouping objects

## -- E --

elementLengths-method | CompressedList objects
elementLengths-method | GappedRanges objects
elementLengths-method | Interval Search Forests
elementLengths-method | Nested Containment List objects
elementLengths-method | Data on ranges
elementLengths-method | Ranges objects
elementLengths-method | Views objects
end-method | GappedRanges objects
end-method | Grouping objects
end-method | List of IRanges and NormalIRanges
end-method | Interval Search Forests
end-method | Interval Search Trees
end-method | Nested Containment List objects
end-method | Data on ranges
end-method | Ranges objects
end-method | List of Ranges
end-method | Views objects
end-method | List of Views
end<- | Ranges objects
end<--method | IRanges and NormalIRanges objects
end<--method | Data on ranges
end<--method | List of Ranges
end<--method | Views objects
endoapply-method | CompressedList objects
endoapply-method | Data on ranges
eval | Vector objects (old man page)
eval-method | Collection of Filter Rules
eval-method | Vector objects (old man page)
evalSeparately | Collection of Filter Rules
evalSeparately-method | Collection of Filter Rules
expand | The expand method for uncompressing compressed data columns
expand-method | The expand method for uncompressing compressed data columns
extractList | Group elements of a vector-like object into a list-like object
extractList-method | Group elements of a vector-like object into a list-like object

## -- F --

FactorList | Lists of Atomic Vectors in Natural and Rle Form
FactorList-class | Lists of Atomic Vectors in Natural and Rle Form
FilterMatrix | Matrix for Filter Results
FilterMatrix-class | Matrix for Filter Results
FilterRules | Collection of Filter Rules
filterRules | Applying over spaces
FilterRules-class | Collection of Filter Rules
filterRules-method | Matrix for Filter Results
filterRules-method | Applying over spaces
filterRules<- | Applying over spaces
filterRules<--method | Applying over spaces
findOverlaps | Finding overlapping ranges
findOverlaps-method | Finding overlapping ranges
findOverlaps-methods | Finding overlapping ranges
findRange | Rle objects (old man page)
findRange-method | Rle objects (old man page)
flank | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
flank-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
follow | Finding the nearest range neighbor
follow-method | Finding the nearest range neighbor

## -- G --

GappedRanges | GappedRanges objects
GappedRanges-class | GappedRanges objects
gaps | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
gaps-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
Grouping | Grouping objects
Grouping-class | Grouping objects
grouplength | Grouping objects
grouplength-method | Grouping objects
grouprank | Grouping objects
grouprank-method | Grouping objects
gsub-method | Lists of Atomic Vectors in Natural and Rle Form

## -- H --

H2LGrouping | Grouping objects
H2LGrouping-class | Grouping objects
high2low | Grouping objects
high2low-method | Grouping objects
Hits-examples | Examples of basic manipulation of Hits objects
HitsList | List of Hits objects
HitsList-class | List of Hits objects

## -- I --

IntegerList | Lists of Atomic Vectors in Natural and Rle Form
IntegerList-class | Lists of Atomic Vectors in Natural and Rle Form
inter-range-methods | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
intersect-method | Set operations on IRanges and RangesList objects
IntervalForest | Interval Search Forests
IntervalForest-class | Interval Search Forests
IntervalTree | Interval Search Trees
IntervalTree-class | Interval Search Trees
intra-range-methods | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
IQR-method | Lists of Atomic Vectors in Natural and Rle Form
IRanges | The IRanges constructor and supporting functions
IRanges-class | IRanges and NormalIRanges objects
IRanges-constructor | The IRanges constructor and supporting functions
IRanges-utils | IRanges utility functions
IRangesList | List of IRanges and NormalIRanges
IRangesList-class | List of IRanges and NormalIRanges
isDisjoint | Ranges objects
isDisjoint-method | IRanges and NormalIRanges objects
isDisjoint-method | Ranges objects
isDisjoint-method | List of Ranges
isEmpty-method | IRanges and NormalIRanges objects
isEmpty-method | Ranges objects
isNormal | Ranges objects
isNormal-method | IRanges and NormalIRanges objects
isNormal-method | List of IRanges and NormalIRanges
isNormal-method | Ranges objects
isNormal-method | List of Ranges
iteratorFun | Applying over spaces
iteratorFun-method | Applying over spaces
iteratorFun<- | Applying over spaces
iteratorFun<--method | Applying over spaces

## -- L --

lapply-method | Lists of Atomic Vectors in Natural and Rle Form
lapply-method | CompressedList objects
lapply-method | Data on ranges
length-method | CompressedList objects
length-method | GappedRanges objects
length-method | Grouping objects
length-method | Interval Search Forests
length-method | Interval Search Trees
length-method | MaskCollection objects
length-method | Nested Containment List objects
length-method | Data on ranges
length-method | Ranges objects
length-method | Views objects
length<--method | Grouping 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-method | Grouping objects

## -- M --

mad-method | Lists of Atomic Vectors in Natural and Rle Form
ManyToOneGrouping | Grouping objects
ManyToOneGrouping-class | Grouping objects
mapCoords | Mapping of ranges to another sequence
mapCoords-methods | Mapping of ranges to another sequence
mapOrder | Grouping objects
mapOrder-method | Grouping objects
Mask | MaskCollection objects
MaskCollection | MaskCollection objects
MaskCollection-class | MaskCollection objects
MaskCollection.show_frame | MaskCollection objects
maskedratio | MaskCollection objects
maskedratio-method | MaskCollection objects
maskedwidth | MaskCollection objects
maskedwidth-method | MaskCollection objects
match-method | Comparing and ordering ranges
Math-method | Lists of Atomic Vectors in Natural and Rle Form
Math2-method | Lists of Atomic Vectors in Natural and Rle Form
max-method | IRanges and NormalIRanges objects
max-method | List of IRanges and NormalIRanges
max-method | MaskCollection objects
max-method | Summarize views on a vector-like object with numeric values
mean-method | Lists of Atomic Vectors in Natural and Rle Form
mean-method | Summarize views on a vector-like object with numeric values
median-method | Lists of Atomic Vectors in Natural and Rle Form
members | Grouping objects
members-method | Grouping objects
mendoapply-method | CompressedList objects
merge-method | List of Ranges
mergeByOverlaps | Finding overlapping ranges
mid | Ranges objects
mid-method | Ranges objects
min-method | IRanges and NormalIRanges objects
min-method | List of IRanges and NormalIRanges
min-method | MaskCollection objects
min-method | Summarize views on a vector-like object with numeric values
mseqapply | Apply function and cast to Vector
mstack | Vector objects (old man page)
mstack-method | Common operations on DataFrame objects
mstack-method | Vector objects (old man page)
multisplit | Split elements belonging to multiple groups

## -- N --

names-method | CompressedList objects
names-method | GappedRanges objects
names-method | Grouping objects
names-method | IRanges and NormalIRanges objects
names-method | Interval Search Forests
names-method | MaskCollection objects
names-method | Nested Containment List objects
names-method | Data on ranges
names-method | Views objects
names<--method | CompressedList objects
names<--method | GappedRanges objects
names<--method | Grouping objects
names<--method | IRanges and NormalIRanges objects
names<--method | MaskCollection objects
names<--method | Data on ranges
names<--method | Views objects
narrow | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
narrow-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
nchar-method | Lists of Atomic Vectors in Natural and Rle Form
NCList | Nested Containment List objects
NCList-class | Nested Containment List objects
NCLists | Nested Containment List objects
NCLists-class | Nested Containment List objects
ncol-method | List of DataFrames
ncol-method | Data on ranges
nearest | Finding the nearest range neighbor
nearest-method | Finding the nearest range neighbor
nearest-methods | Finding the nearest range neighbor
newViews | Views objects
ngap | GappedRanges objects
ngap-method | GappedRanges objects
nir_list | MaskCollection objects
nir_list-method | MaskCollection objects
nobj | Grouping objects
nobj-method | Grouping objects
NormalIRanges | IRanges and NormalIRanges objects
NormalIRanges-class | IRanges and NormalIRanges objects
NormalIRangesList | List of IRanges and NormalIRanges
NormalIRangesList-class | List of IRanges and NormalIRanges
nrow-method | List of DataFrames
nrow-method | Data on ranges
NumericList | Lists of Atomic Vectors in Natural and Rle Form
NumericList-class | Lists of Atomic Vectors in Natural and Rle Form

## -- O --

Ops-method | Lists of Atomic Vectors in Natural and Rle Form
Ops-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
order-method | Lists of Atomic Vectors in Natural and Rle Form
order-method | Comparing and ordering ranges
overlapsAny | Finding overlapping ranges
overlapsAny-method | Finding overlapping ranges

## -- P --

params | Collection of Filter Rules
params-method | Collection of Filter Rules
Partitioning | Grouping objects
Partitioning-class | Grouping objects
PartitioningByEnd | Grouping objects
PartitioningByEnd-class | Grouping objects
PartitioningByWidth | Grouping objects
PartitioningByWidth-class | Grouping objects
PartitioningMap | Grouping objects
PartitioningMap-class | Grouping objects
pgap | Set operations on IRanges and RangesList objects
pgap-method | Set operations on IRanges and RangesList objects
pintersect | Set operations on IRanges and RangesList objects
pintersect-method | Set operations on IRanges and RangesList objects
pmapCoords | Mapping of ranges to another sequence
pmax-method | Lists of Atomic Vectors in Natural and Rle Form
pmax.int-method | Lists of Atomic Vectors in Natural and Rle Form
pmin-method | Lists of Atomic Vectors in Natural and Rle Form
pmin.int-method | Lists of Atomic Vectors in Natural and Rle Form
precede | Finding the nearest range neighbor
precede-method | Finding the nearest range neighbor
promoters | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
promoters-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
psetdiff | Set operations on IRanges and RangesList objects
psetdiff-method | Set operations on IRanges and RangesList objects
punion | Set operations on IRanges and RangesList objects
punion-method | Set operations on IRanges and RangesList objects

## -- Q --

quantile-method | Lists of Atomic Vectors in Natural and Rle Form
queryHits-method | List of Hits objects
queryLength-method | List of Hits objects

## -- R --

range | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
range-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
rangeComparisonCodeToLetter | Comparing and ordering ranges
RangedData | Data on ranges
rangedData | Applying over spaces
RangedData-class | Data on ranges
rangedData-method | Applying over spaces
rangedData<- | Applying over spaces
rangedData<--method | Applying over spaces
RangedDataList | Lists of RangedData
RangedDataList-class | Lists of RangedData
RangedSelection | Selection of ranges and columns
RangedSelection-class | Selection of ranges and columns
Ranges | Ranges objects
ranges | Views objects
Ranges-class | Ranges objects
Ranges-comparison | Comparing and ordering ranges
ranges-method | Lists of Atomic Vectors in Natural and Rle Form
ranges-method | List of Hits objects
ranges-method | Nested Containment List objects
ranges-method | Data on ranges
ranges-method | Selection of ranges and columns
ranges-method | Rle objects (old man page)
ranges-method | Views objects
ranges-method | List of Views
ranges-method | Finding overlapping ranges
ranges<- | Views objects
ranges<--method | Data on ranges
ranges<--method | Selection of ranges and columns
ranges<--method | Views objects
RangesList | List of Ranges
RangesList-class | List of Ranges
RangesORmissing | Finding the nearest range neighbor
RangesORmissing-class | Finding the nearest range neighbor
rank-method | Lists of Atomic Vectors in Natural and Rle Form
RawList | Lists of Atomic Vectors in Natural and Rle Form
RawList-class | Lists of Atomic Vectors in Natural and Rle Form
rbind-method | List of DataFrames
rbind-method | Matrix for Filter Results
rbind-method | Data on ranges
rdapply | Applying over spaces
rdapply-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 | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
reduce-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
reducerFun | Applying over spaces
reducerFun-method | Applying over spaces
reducerFun<- | Applying over spaces
reducerFun<--method | Applying over spaces
reducerParams | Applying over spaces
reducerParams-method | Applying over spaces
reducerParams<- | Applying over spaces
reducerParams<--method | Applying over spaces
reflect | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
reflect-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
relist-method | Group elements of a vector-like object into a list-like object
relistToClass | Group elements of a vector-like object into a list-like object
relistToClass-method | Group elements of a vector-like object into a list-like object
rep-method | Vector objects (old man page)
rep.int-method | Vector objects (old man page)
resize | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
resize-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
restrict | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
restrict-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
rev-method | Vector objects (old man page)
revElements-method | CompressedList objects
reverse | reverse
reverse-method | reverse
RleList | Lists of Atomic Vectors in Natural and Rle Form
RleList-class | Lists of Atomic Vectors in Natural and Rle Form
RleList-method | 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-method | List of DataFrames
rownames-method | Data on ranges
rownames<--method | List of DataFrames
rownames<--method | Data on ranges
runLength-method | Lists of Atomic Vectors in Natural and Rle Form
runmean-method | Lists of Atomic Vectors in Natural and Rle Form
runmed-method | Lists of Atomic Vectors in Natural and Rle Form
runq-method | Lists of Atomic Vectors in Natural and Rle Form
runsum-method | Lists of Atomic Vectors in Natural and Rle Form
runValue-method | Lists of Atomic Vectors in Natural and Rle Form
runValue<--method | Lists of Atomic Vectors in Natural and Rle Form
runwtsum-method | Lists of Atomic Vectors in Natural and Rle Form

## -- S --

score-method | Data on ranges
score<--method | Data on ranges
sd-method | Lists of Atomic Vectors in Natural and Rle Form
selfmatch-method | Comparing and ordering ranges
seqapply | Apply function and cast to Vector
seqby | Apply function and cast to Vector
seqsplit | Apply function and cast to Vector
setdiff-method | Set operations on IRanges and RangesList objects
setops-methods | Set operations on IRanges and RangesList objects
shift | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
shift-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
shiftApply | Vector objects (old man page)
shiftApply-method | Vector objects (old man page)
show-method | Lists of Atomic Vectors in Natural and Rle Form
show-method | List of DataFrames
show-method | Matrix for Filter Results
show-method | Collection of Filter Rules
show-method | GappedRanges objects
show-method | Grouping objects
show-method | Interval Search Forests
show-method | MaskCollection objects
show-method | Data on ranges
show-method | Ranges objects
show-method | List of Ranges
show-method | The RleViews class
showAsCell-method | Lists of Atomic Vectors in Natural and Rle Form
showAsCell-method | Ranges objects
showAsCell-method | List of Ranges
showAsCell-method | Vector objects (old man page)
SimpleAtomicList | Lists of Atomic Vectors in Natural and Rle Form
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
SimpleFactorList | Lists of Atomic Vectors in Natural and Rle Form
SimpleFactorList-class | Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList | Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class | Lists of Atomic Vectors in Natural and Rle Form
SimpleIRangesList | List of IRanges and NormalIRanges
SimpleIRangesList-class | List of IRanges and NormalIRanges
SimpleLogicalList | Lists of Atomic Vectors in Natural and Rle Form
SimpleLogicalList-class | Lists of Atomic Vectors in Natural and Rle Form
SimpleNormalIRangesList | List of IRanges and NormalIRanges
SimpleNormalIRangesList-class | List of IRanges and NormalIRanges
SimpleNumericList | Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList-class | Lists of Atomic Vectors in Natural and Rle Form
SimpleRangesList | List of Ranges
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
SimpleViewsList | List of Views
SimpleViewsList-class | List of Views
simplify | Applying over spaces
simplify-method | Applying over spaces
simplify<- | Applying over spaces
simplify<--method | Applying over spaces
slice | Slice a vector-like or list-like object
slice-method | Slice a vector-like or list-like object
slice-methods | Slice a vector-like or list-like object
smoothEnds-method | Lists of Atomic Vectors in Natural and Rle Form
solveUserSEW | The IRanges constructor and supporting functions
solveUserSEW0 | The IRanges constructor and supporting functions
sort-method | Lists of Atomic Vectors in Natural and Rle Form
sort.List | Lists of Atomic Vectors in Natural and Rle Form
space | List of Ranges
space-method | List of Hits objects
space-method | Data on ranges
space-method | List of Ranges
split-method | Data on ranges
split-method | Group elements of a vector-like object into a list-like object
split<--method | Apply function and cast to Vector
splitAsList | Group elements of a vector-like object into a list-like object
splitAsList,ANY,List | Group elements of a vector-like object into a list-like object
splitAsList,ANY,Rle | Group elements of a vector-like object into a list-like object
splitAsList,ANY,vectorORfactor | Group elements of a vector-like object into a list-like object
SplitDataFrameList | List of DataFrames
SplitDataFrameList-class | List of DataFrames
splitRanges | Rle objects (old man page)
splitRanges-method | Rle objects (old man page)
stack-method | List of DataFrames
stack-method | List objects (old man page)
stack-method | Lists of RangedData
start-method | GappedRanges objects
start-method | Grouping objects
start-method | IRanges and NormalIRanges objects
start-method | List of IRanges and NormalIRanges
start-method | Interval Search Forests
start-method | Interval Search Trees
start-method | Nested Containment List objects
start-method | Data on ranges
start-method | Ranges objects
start-method | List of Ranges
start-method | Views objects
start-method | List of Views
start<- | Ranges objects
start<--method | IRanges and NormalIRanges objects
start<--method | Data on ranges
start<--method | List of Ranges
start<--method | Views objects
sub-method | Lists of Atomic Vectors in Natural and Rle Form
subject | Views objects
subject-method | List of RleViews
subject-method | Views objects
subjectHits-method | List of Hits objects
subjectLength-method | List of Hits objects
subset-method | Vector objects (old man page)
subsetByFilter | Collection of Filter Rules
subsetByFilter-method | Collection of Filter Rules
subsetByOverlaps | Finding overlapping ranges
subsetByOverlaps-method | Finding overlapping ranges
subviews | Views objects
subviews-method | Views objects
successiveIRanges | IRanges utility functions
successiveViews | Views objects
sum-method | Lists of Atomic Vectors in Natural and Rle Form
sum-method | Summarize views on a vector-like object with numeric values
Summary-method | Lists of Atomic Vectors in Natural and Rle Form
Summary-method | Summarize views on a vector-like object with numeric values
summary-method | Matrix for Filter Results
summary-method | Collection of Filter Rules
summary-method | List of IRanges and NormalIRanges

## -- T --

t-method | List of Hits objects
table-method | Lists of Atomic Vectors in Natural and Rle Form
tapply-method | Vector objects (old man page)
threebands | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
threebands-method | Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
tile | Ranges objects
tile-method | Ranges objects
togroup | Grouping objects
togroup-method | Grouping objects
togrouplength | Grouping objects
togrouplength-method | Grouping objects
togrouprank | Grouping objects
togrouprank-method | Grouping objects
tolower-method | Lists of Atomic Vectors in Natural and Rle Form
toupper-method | Lists of Atomic Vectors in Natural and Rle Form
transform-method | List of DataFrames
trim | Views objects
trim-method | Views objects
tseqapply | Apply function and cast to Vector

## -- U --

union-method | Set operations on IRanges and RangesList objects
unique-method | Lists of Atomic Vectors in Natural and Rle Form
unique.CompressedList | Lists of Atomic Vectors in Natural and Rle Form
unique.RleList | Lists of Atomic Vectors in Natural and Rle Form
universe | List of Ranges
universe-method | Data on ranges
universe-method | List of Ranges
universe-method | List of Views
universe<- | List of Ranges
universe<--method | Data on ranges
universe<--method | List of Ranges
universe<--method | List of Views
unlist,SimpleFactorList | Lists of Atomic Vectors in Natural and Rle Form
unlist,SimpleRleList | Lists of Atomic Vectors in Natural and Rle Form
unlist-method | CompressedList objects
unlist-method | List of IRanges and NormalIRanges
unlist-method | Lists of RangedData
unlist-method | Ranges objects
unsplit-method | Apply function and cast to Vector
unstrsplit-method | Lists of Atomic Vectors in Natural and Rle Form
update-method | IRanges and NormalIRanges objects
update-method | Ranges objects
updateObject-method | Update an object of a class defined in the IRanges package to its current class definition
updateObject-methods | Update an object of a class defined in the IRanges package to its current class definition

## -- V --

values-method | Data on ranges
values<--method | Data on ranges
var-method | Lists of Atomic Vectors in Natural and Rle Form
view-summarization-methods | Summarize views on a vector-like object with numeric values
viewApply | Summarize views on a vector-like object with numeric values
viewApply-method | Summarize views on a vector-like object with numeric values
viewMaxs | Summarize views on a vector-like object with numeric values
viewMaxs-method | Summarize views on a vector-like object with numeric values
viewMeans | Summarize views on a vector-like object with numeric values
viewMeans-method | Summarize views on a vector-like object with numeric values
viewMins | Summarize views on a vector-like object with numeric values
viewMins-method | Summarize views on a vector-like object with numeric values
viewRangeMaxs | Summarize views on a vector-like object with numeric values
viewRangeMaxs-method | Summarize views on a vector-like object with numeric values
viewRangeMins | Summarize views on a vector-like object with numeric values
viewRangeMins-method | Summarize views on a vector-like object with numeric values
Views | Views objects
Views-class | Views objects
Views-method | The RleViews class
Views-method | List of RleViews
ViewsList | List of Views
ViewsList-class | List of Views
viewSums | Summarize views on a vector-like object with numeric values
viewSums-method | Summarize views on a vector-like object with numeric values
viewWhichMaxs | Summarize views on a vector-like object with numeric values
viewWhichMaxs-method | Summarize views on a vector-like object with numeric values
viewWhichMins | Summarize views on a vector-like object with numeric values
viewWhichMins-method | Summarize views on a vector-like object with numeric values
vmembers | Grouping objects
vmembers-method | Grouping objects

## -- W --

which-method | Lists of Atomic Vectors in Natural and Rle Form
which.max-method | Lists of Atomic Vectors in Natural and Rle Form
which.max-method | Summarize views on a vector-like object with numeric values
which.min-method | Lists of Atomic Vectors in Natural and Rle Form
which.min-method | Summarize views on a vector-like object with numeric values
whichAsIRanges | IRanges utility functions
whichFirstNotNormal | Ranges objects
whichFirstNotNormal-method | Ranges objects
whichFirstNotNormal-method | List of Ranges
width | Ranges objects
width-method | Grouping objects
width-method | IRanges and NormalIRanges objects
width-method | List of IRanges and NormalIRanges
width-method | Interval Search Forests
width-method | MaskCollection objects
width-method | Nested Containment List objects
width-method | Data on ranges
width-method | Ranges objects
width-method | List of Ranges
width-method | Views objects
width-method | List of Views
width<- | Ranges objects
width<--method | IRanges and NormalIRanges objects
width<--method | Data on ranges
width<--method | List of Ranges
width<--method | Views objects
window-method | Rle objects (old man page)
window.Rle | Rle objects (old man page)
window<--method | Vector objects (old man page)
window<-.factor | Vector objects (old man page)
window<-.Vector | Vector objects (old man page)
window<-.vector | Vector objects (old man page)
with-method | Vector objects (old man page)
within-method | Data on ranges

## -- misc --

!-method | CompressedList objects
$<--method | CompressedList objects
$<--method | Data on ranges
%outside% | Finding overlapping ranges
%over% | Finding overlapping ranges
%within% | Finding overlapping ranges
[-method | List of DataFrames
[-method | Matrix for Filter Results
[-method | Collection of Filter Rules
[-method | Interval Search Forests
[-method | Data on ranges
[<--method | List of DataFrames
[[-method | List of DataFrames
[[-method | Data on ranges
[[<--method | CompressedList objects
[[<--method | List of DataFrames
[[<--method | Collection of Filter Rules
[[<--method | Data on ranges