# Infrastructure for manipulating intervals on sequences

## Documentation for package ‘IRanges’ version 1.16.6

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- 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 X 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
aggregate-method | External Data Frame
aggregate-method | The DataTable API
aggregate-method | Rle objects
aggregate-method | Simple and Compressed List Classes
aggregate-method | Vector objects
all-method | Lists of Atomic Vectors in Natural and Rle Form
Annotated | Annotated class
Annotated-class | Annotated class
append-method | Collection of Filter Rules
append-method | MaskCollection objects
append-method | Vector 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.character-method | Rle objects
as.character-method | Vector objects
as.complex-method | Rle objects
as.complex-method | Vector objects
as.data.frame-method | External Data Frame
as.data.frame-method | List of DataFrames
as.data.frame-method | GappedRanges objects
as.data.frame-method | Set of hits between 2 vector-like objects
as.data.frame-method | OverlapEncodings objects
as.data.frame-method | Data on ranges
as.data.frame-method | Ranges objects
as.data.frame-method | List of Ranges
as.data.frame-method | Rle objects
as.data.frame-method | Vector objects
as.data.frame-method | XVectorList objects
as.double-method | Vector objects
as.env | List objects
as.env-method | The DataTable API
as.env-method | List objects
as.env-method | Data on ranges
as.factor-method | Rle objects
as.integer-method | Ranges objects
as.integer-method | Rle objects
as.integer-method | Vector objects
as.integer-method | XVector objects
as.list-method | Lists of Atomic Vectors in Natural and Rle Form
as.list-method | Set of hits between 2 vector-like objects
as.list-method | List of IRanges and NormalIRanges
as.list-method | List objects
as.list-method | Rle objects
as.list-method | Simple and Compressed List Classes
as.logical-method | Rle objects
as.logical-method | Vector objects
as.matrix-method | External Data Frame
as.matrix-method | Set of hits between 2 vector-like objects
as.matrix-method | List of Hits objects
as.matrix-method | Ranges objects
as.matrix-method | Views objects
as.matrix-method | List of Views
as.numeric-method | Rle objects
as.numeric-method | Vector objects
as.numeric-method | XVector objects
as.raw-method | Rle objects
as.raw-method | Vector objects
as.raw-method | XVector objects
as.table-method | Set of hits between 2 vector-like objects
as.table-method | List of Hits objects
as.vector-method | Lists of Atomic Vectors in Natural and Rle Form
as.vector-method | Rle objects
as.vector-method | XVector objects
as.vectorORfactor | Rle objects
as.vectorORfactor-method | Rle objects
asNormalIRanges | IRanges utility functions
AtomicList-class | Lists of Atomic Vectors in Natural and Rle Form

## -- B --

breakInChunks | IRanges utility functions
by-method | The DataTable API

## -- C --

c-method | Collection of Filter Rules
c-method | GappedRanges objects
c-method | IRanges and NormalIRanges objects
c-method | Data on ranges
c-method | Rle objects
c-method | Simple and Compressed List Classes
c-method | Vector objects
c-method | XVector objects
c-method | XVectorList objects
cbind-method | External Data Frame
cbind-method | List of DataFrames
cbind-method | The DataTable API
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
chartr-method | Rle objects
class:CompressedIRangesList | List of IRanges and NormalIRanges
class:CompressedNormalIRangesList | List of IRanges and NormalIRanges
class:DataFrame | External Data Frame
class:DataTable | The DataTable API
class:DataTableORNULL | The DataTable API
class:Dups | Grouping objects
class:GappedRanges | GappedRanges objects
class:GroupedIRanges | XVectorList objects
class:Grouping | Grouping objects
class:H2LGrouping | Grouping objects
class:IRanges | IRanges and NormalIRanges objects
class:IRangesList | List of IRanges and NormalIRanges
class:List | List objects
class:MaskCollection | MaskCollection objects
class:NormalIRanges | IRanges and NormalIRanges objects
class:NormalIRangesList | List of IRanges and NormalIRanges
class:OverlapEncodings | OverlapEncodings objects
class:Partitioning | Grouping objects
class:PartitioningByEnd | Grouping objects
class:PartitioningByWidth | 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:Rle | Rle objects
class:RleViews | The RleViews class
class:SimpleIRangesList | List of IRanges and NormalIRanges
class:SimpleNormalIRangesList | List of IRanges and NormalIRanges
class:SimpleRangesList-class | List of Ranges
class:SimpleViewsList | List of Views
class:Vector | Vector objects
class:Views | Views objects
class:ViewsList | List of Views
class:XDouble | XVector objects
class:XDoubleViews | The XDoubleViews class
class:XInteger | XVector objects
class:XIntegerViews | The XIntegerViews class
class:XRaw | XVector objects
class:XRawList | XRawList objects
class:XVector | XVector objects
class:XVectorList | XVectorList objects
coerce-method | Lists of Atomic Vectors in Natural and Rle Form
coerce-method | External Data Frame
coerce-method | List of DataFrames
coerce-method | GappedRanges objects
coerce-method | Grouping objects
coerce-method | Set of hits between 2 vector-like objects
coerce-method | IRanges and NormalIRanges objects
coerce-method | IRanges utility functions
coerce-method | List of IRanges and NormalIRanges
coerce-method | Interval Search Trees
coerce-method | List objects
coerce-method | MaskCollection objects
coerce-method | Data on ranges
coerce-method | Selection of ranges and columns
coerce-method | List of Ranges
coerce-method | Mapping of ranges to another sequence
coerce-method | Rle objects
coerce-method | The RleViews class
coerce-method | List of RleViews
coerce-method | Simple and Compressed List Classes
coerce-method | Vector objects
coerce-method | Views objects
coerce-method | XVector objects
collapse | MaskCollection objects
collapse-method | MaskCollection objects
colnames-method | External Data Frame
colnames-method | List of DataFrames
colnames-method | Data on ranges
colnames-method | Selection of ranges and columns
colnames<--method | External Data Frame
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
compact | Object compaction
compact-method | Object compaction
compare | Comparing and ordering ranges
compare-method | Comparing and ordering ranges
complete.cases-method | The DataTable API
Complex-method | Lists of Atomic Vectors in Natural and Rle Form
Complex-method | Rle objects
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 | List of IRanges and NormalIRanges
CompressedIRangesList-class | List of IRanges and NormalIRanges
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
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
cor-method | Rle objects
countOverlaps | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
countOverlaps-method | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
countQueryHits | Set of hits between 2 vector-like objects
countQueryHits-method | Set of hits between 2 vector-like objects
countSubjectHits | Set of hits between 2 vector-like objects
countSubjectHits-method | Set of hits between 2 vector-like objects
cov-method | Lists of Atomic Vectors in Natural and Rle Form
cov-method | Rle objects
coverage | Coverage across a set of ranges
coverage-method | Coverage across 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 | External Data Frame
DataFrame-class | External Data Frame
DataFrameList | List of DataFrames
DataFrameList-class | List of DataFrames
DataTable | The DataTable API
DataTable-API | The DataTable API
DataTable-class | The DataTable API
DataTable-stats | Statistical modeling with DataTable
DataTableORNULL | The DataTable API
DataTableORNULL-class | The DataTable API
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
diff-method | Rle objects
dim-method | List of DataFrames
dim-method | The DataTable API
dim-method | Set of hits between 2 vector-like objects
dim-method | Mapping of ranges to another sequence
dimnames-method | List of DataFrames
dimnames-method | The DataTable API
dimnames<--method | List of DataFrames
dimnames<--method | The DataTable API
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 | The DataTable API
duplicated-method | Grouping objects
duplicated-method | Comparing and ordering ranges
Dups | Grouping objects
Dups-class | Grouping objects

## -- E --

elementLengths | List objects
elementLengths-method | GappedRanges objects
elementLengths-method | List objects
elementLengths-method | Data on ranges
elementLengths-method | Ranges objects
elementLengths-method | Views objects
elementMetadata | Vector objects
elementMetadata-method | Vector objects
elementMetadata<- | Vector objects
elementMetadata<--method | Vector objects
elementType | List objects
elementType-method | List objects
encodeOverlaps | Compute overlap encodings
encodeOverlaps-method | Compute overlap encodings
encodeOverlaps1 | Compute overlap encodings
encoding | OverlapEncodings objects
encoding-method | OverlapEncodings objects
end-method | GappedRanges objects
end-method | Grouping objects
end-method | List of IRanges and NormalIRanges
end-method | Interval Search Trees
end-method | Data on ranges
end-method | Ranges objects
end-method | List of Ranges
end-method | Rle objects
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 | Endomorphisms via application of a function over an object's elements
endoapply-method | List objects
endoapply-method | Data on ranges
endoapply-method | Simple and Compressed List Classes
endoapply-method | Endomorphisms via application of a function over an object's elements
eval | List objects
eval-method | Collection of Filter Rules
eval-method | List objects
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

## -- F --

Filter-method | Functional programming methods for List objects
FilterRules | Collection of Filter Rules
filterRules | Applying over spaces
FilterRules-class | Collection of Filter Rules
filterRules-method | Applying over spaces
filterRules<- | Applying over spaces
filterRules<--method | Applying over spaces
Find-method | Functional programming methods for List objects
findOverlaps | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
findOverlaps-method | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
findOverlaps-methods | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
findRange | Rle objects
findRange-method | Rle objects
findRun | Rle objects
findRun-method | Rle objects
first | Ranges objects
first-method | Ranges objects
flank | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
flank-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
flippedQuery | OverlapEncodings objects
flippedQuery-method | OverlapEncodings objects
follow | Finding the nearest range neighbor
follow-method | Finding the nearest range neighbor
funprog-methods | Functional programming methods for List objects

## -- 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
GroupedIRanges | XVectorList objects
GroupedIRanges-class | XVectorList objects
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
gsub-method | Rle objects

## -- H --

H2LGrouping | Grouping objects
H2LGrouping-class | Grouping objects
head-method | The DataTable API
head-method | Vector objects
high2low | Grouping objects
high2low-method | Grouping objects
Hits | Set of hits between 2 vector-like objects
hits | Mapping of ranges to another sequence
Hits-class | Set of hits between 2 vector-like objects
HitsList-class | List of Hits objects

## -- I --

ifelse-method | Rle objects
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 of hits between 2 vector-like objects
intersect-method | Set operations on IRanges objects
intersect-method | List of IRanges and NormalIRanges
intersect-method | RangesList utility functions
IntervalTree | Interval Search Trees
IntervalTree-class | Interval Search Trees
intra-range-methods | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
IQR-method | Lists of Atomic Vectors in Natural and Rle Form
IQR-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 and NormalIRanges
IRangesList-class | List of IRanges and NormalIRanges
is.na-method | Lists of Atomic Vectors in Natural and Rle Form
is.na-method | The DataTable API
is.na-method | Rle objects
is.unsorted-method | Rle objects
isConstant | Test if an atomic vector or array is constant
isConstant-method | Test if an atomic vector or array is constant
isDisjoint | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
isDisjoint-method | Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
isEmpty | List objects
isEmpty-method | IRanges and NormalIRanges objects
isEmpty-method | List objects
isEmpty-method | Ranges objects
isEmpty-method | Simple and Compressed List Classes
isNormal | Ranges objects
isNormal-method | IRanges and NormalIRanges objects
isNormal-method | List of IRanges and NormalIRanges
isNormal-method | Ranges objects
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 | List objects
lapply-method | Data on ranges
lapply-method | Simple and Compressed List Classes
last | Ranges objects
last-method | Ranges objects
Lencoding | OverlapEncodings objects
Lencoding-method | OverlapEncodings objects
length-method | GappedRanges objects
length-method | Grouping objects
length-method | Set of hits between 2 vector-like objects
length-method | Interval Search Trees
length-method | MaskCollection objects
length-method | OverlapEncodings objects
length-method | Data on ranges
length-method | Ranges objects
length-method | Mapping of ranges to another sequence
length-method | Rle objects
length-method | Simple and Compressed List Classes
length-method | Views objects
length-method | XVector objects
length-method | XVectorList objects
length<--method | Grouping objects
levels-method | OverlapEncodings objects
levels-method | Rle objects
levels<--method | Rle objects
List | List objects
List-class | List objects
Lngap | OverlapEncodings objects
Lngap-method | OverlapEncodings objects
Loffset | OverlapEncodings objects
Loffset-method | OverlapEncodings 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
mad-method | Rle objects
map | Mapping of ranges to another sequence
Map-method | Functional programming methods for List objects
mapply-method | List 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 | Lists of Atomic Vectors in Natural and Rle Form
match-method | Set of hits between 2 vector-like objects
match-method | Rle objects
match-method | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
matchMatrix | Set of hits between 2 vector-like objects
Math-method | Lists of Atomic Vectors in Natural and Rle Form
Math-method | Rle objects
Math2-method | Lists of Atomic Vectors in Natural and Rle Form
Math2-method | Rle objects
max-method | IRanges and NormalIRanges objects
max-method | List of IRanges and NormalIRanges
max-method | MaskCollection objects
max-method | Utility functions and numeric summary of Views of numerics
mcols | Vector objects
mcols-method | Vector objects
mcols<- | Vector objects
mcols<--method | Vector objects
mean-method | Lists of Atomic Vectors in Natural and Rle Form
mean-method | Rle objects
mean-method | Utility functions and numeric summary of Views of numerics
median-method | Lists of Atomic Vectors in Natural and Rle Form
median-method | Rle objects
members | Grouping objects
members-method | Grouping objects
mendoapply | Endomorphisms via application of a function over an object's elements
mendoapply-method | List objects
mendoapply-method | Simple and Compressed List Classes
mendoapply-method | Endomorphisms via application of a function over an object's elements
merge-method | The DataTable API
merge-method | RangesList utility functions
metadata | Annotated class
metadata-method | Annotated class
metadata<- | Annotated class
metadata<--method | Annotated class
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 | Utility functions and numeric summary of Views of numerics
mseqapply | Apply function and cast to Vector
mstack | Vector objects
mstack-method | Vector objects
multisplit | Split elements belonging to multiple groups

## -- N --

na.exclude | The DataTable API
na.exclude-method | The DataTable API
na.omit | The DataTable API
na.omit-method | The DataTable API
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 | Simple and Compressed List Classes
names-method | Views objects
names-method | XVectorList 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 | Simple and Compressed List Classes
names<--method | Views objects
names<--method | XVectorList objects
narrow | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
narrow-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
nchar-method | Lists of Atomic Vectors in Natural and Rle Form
nchar-method | Rle objects
NCOL-method | The DataTable API
ncol-method | External Data Frame
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
ngap-method | OverlapEncodings objects
nir_list | MaskCollection objects
nir_list-method | MaskCollection objects
nlevels-method | Vector 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 | The DataTable API
NROW-method | Vector objects
nrow-method | External Data Frame
nrow-method | List of DataFrames
nrow-method | Data on ranges
nrun | Rle objects
nrun-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-method | Lists of Atomic Vectors in Natural and Rle Form
Ops-method | Rle objects
Ops-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
order-method | Comparing and ordering ranges
OverlapEncodings | OverlapEncodings objects
OverlapEncodings-class | OverlapEncodings objects

## -- 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
paste-method | Rle objects
pgap | Set operations on IRanges objects
pgap-method | Set operations on IRanges objects
pintersect | Set operations on IRanges objects
pintersect-method | Set operations on IRanges objects
pmap | Mapping of ranges to another sequence
pmax-method | Lists of Atomic Vectors in Natural and Rle Form
pmax-method | Rle objects
pmax.int-method | Lists of Atomic Vectors in Natural and Rle Form
pmax.int-method | Rle objects
pmin-method | Lists of Atomic Vectors in Natural and Rle Form
pmin-method | Rle objects
pmin.int-method | Lists of Atomic Vectors in Natural and Rle Form
pmin.int-method | Rle objects
Position-method | Functional programming methods for List objects
precede | Finding the nearest range neighbor
precede-method | Finding the nearest range neighbor
psetdiff | Set operations on IRanges objects
psetdiff-method | Set operations on IRanges objects
punion | Set operations on IRanges objects
punion-method | Set operations on IRanges objects

## -- Q --

quantile-method | Lists of Atomic Vectors in Natural and Rle Form
quantile-method | Rle objects
queryHits | Set of hits between 2 vector-like objects
queryHits-method | Set of hits between 2 vector-like objects
queryHits-method | List of Hits objects
queryHits-method | Mapping of ranges to another sequence
queryLength | Set of hits between 2 vector-like objects
queryLength-method | Set of hits between 2 vector-like objects

## -- R --

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 | Set of hits between 2 vector-like objects
ranges-method | List of Hits objects
ranges-method | Data on ranges
ranges-method | Selection of ranges and columns
ranges-method | Mapping of ranges to another sequence
ranges-method | Rle objects
ranges-method | Views objects
ranges-method | List of Views
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
RangesList-utils | RangesList utility functions
RangesList_encodeOverlaps | Compute overlap encodings
RangesMapping-class | Mapping of ranges to another sequence
RangesORmissing | Finding the nearest range neighbor
RangesORmissing-class | Finding the nearest range neighbor
rank-method | Comparing and ordering ranges
RawList | Lists of Atomic Vectors in Natural and Rle Form
RawList-class | Lists of Atomic Vectors in Natural and Rle Form
rbind-method | External Data Frame
rbind-method | List of DataFrames
rbind-method | The DataTable API
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 | Functional programming methods for List objects
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, MaskCollection, or XVectorList object
reflect-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
relist-method | List objects
remapHits | Set of hits between 2 vector-like objects
rename | Vector objects
rename-method | Vector objects
Rencoding | OverlapEncodings objects
Rencoding-method | OverlapEncodings objects
rep-method | Rle objects
rep-method | Vector objects
rep.int-method | Rle objects
rep.int-method | Vector objects
resize | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
resize-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
restrict | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
restrict-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
rev-method | Rle objects
rev-method | Vector objects
rev-method | reverse
revElements | List objects
revElements-method | List objects
revElements-method | Simple and Compressed List Classes
reverse | reverse
reverse-method | reverse
Rle | Rle objects
Rle-class | Rle objects
Rle-method | Rle objects
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
Rngap | OverlapEncodings objects
Rngap-method | OverlapEncodings objects
Roffset | OverlapEncodings objects
Roffset-method | OverlapEncodings objects
rownames-method | External Data Frame
rownames-method | List of DataFrames
rownames-method | Data on ranges
rownames<--method | External Data Frame
rownames<--method | List of DataFrames
rownames<--method | Data on ranges
runLength | Rle objects
runLength-method | Lists of Atomic Vectors in Natural and Rle Form
runLength-method | Rle objects
runLength<- | Rle objects
runLength<--method | Rle objects
runmean | Fixed width running window summaries across vector-like objects
runmean-method | Lists of Atomic Vectors in Natural and Rle Form
runmean-method | Rle objects
runmed-method | Lists of Atomic Vectors in Natural and Rle Form
runmed-method | Rle objects
runq | Fixed width running window summaries across vector-like objects
runq-method | Lists of Atomic Vectors in Natural and Rle Form
runq-method | Rle objects
runstat | Fixed width running window summaries across vector-like objects
runsum | Fixed width running window summaries across vector-like objects
runsum-method | Lists of Atomic Vectors in Natural and Rle Form
runsum-method | Rle objects
runValue | Rle objects
runValue-method | Lists of Atomic Vectors in Natural and Rle Form
runValue-method | Rle objects
runValue<- | Rle objects
runValue<--method | Rle objects
runwtsum | Fixed width running window summaries across vector-like objects
runwtsum-method | Lists of Atomic Vectors in Natural and Rle Form
runwtsum-method | Rle objects

## -- S --

safeExplode | Low-level string utilities
sapply-method | List objects
score | Score accessor and setter
score-method | Data on ranges
score<- | Score accessor and setter
score<--method | Data on ranges
sd-method | Lists of Atomic Vectors in Natural and Rle Form
sd-method | Rle objects
seqapply | Apply function and cast to Vector
seqby | Apply function and cast to Vector
seqselect | Vector objects
seqselect-method | External Data Frame
seqselect-method | The DataTable API
seqselect-method | GappedRanges objects
seqselect-method | IRanges and NormalIRanges objects
seqselect-method | Data on ranges
seqselect-method | Rle objects
seqselect-method | Simple and Compressed List Classes
seqselect-method | Vector objects
seqselect-method | XVector objects
seqselect-method | XVectorList objects
seqselect<- | Vector objects
seqselect<--method | Lists of Atomic Vectors in Natural and Rle Form
seqselect<--method | The DataTable API
seqselect<--method | IRanges and NormalIRanges objects
seqselect<--method | Data on ranges
seqselect<--method | Rle objects
seqselect<--method | Simple and Compressed List Classes
seqselect<--method | Vector objects
seqsplit | Apply function and cast to Vector
setdiff-method | Set of hits between 2 vector-like objects
setdiff-method | Set operations on IRanges objects
setdiff-method | List of IRanges and NormalIRanges
setdiff-method | RangesList utility functions
shift | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
shift-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
shiftApply | Vector objects
shiftApply-method | Rle objects
shiftApply-method | Vector objects
show-method | Lists of Atomic Vectors in Natural and Rle Form
show-method | List of DataFrames
show-method | The DataTable API
show-method | Collection of Filter Rules
show-method | GappedRanges objects
show-method | Grouping objects
show-method | Set of hits between 2 vector-like objects
show-method | List objects
show-method | MaskCollection objects
show-method | OverlapEncodings objects
show-method | Data on ranges
show-method | Ranges objects
show-method | List of Ranges
show-method | Rle objects
show-method | The RleViews class
show-method | The XDoubleViews class
show-method | The XIntegerViews class
show-method | XVector objects
show-method | XVectorList 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 | List of IRanges and NormalIRanges
SimpleIRangesList-class | List of IRanges and NormalIRanges
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
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 | Utility functions and numeric summary of Views of numerics
slice-method | Utility functions and numeric summary of Views of numerics
smoothEnds-method | Lists of Atomic Vectors in Natural and Rle Form
smoothEnds-method | Rle objects
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-method | Comparing and ordering ranges
sort-method | Rle objects
sort-method | Vector objects
space | List of Ranges
space-method | List of Hits objects
space-method | Data on ranges
space-method | List of Ranges
space-method | Mapping of ranges to another sequence
split-method | Data on ranges
split-method | Vector objects
split<--method | Vector objects
SplitDataFrameList | List of DataFrames
SplitDataFrameList-class | List of DataFrames
splitRanges | Rle objects
splitRanges-method | Rle objects
stack-method | List of DataFrames
stack-method | List objects
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 Trees
start-method | Data on ranges
start-method | Ranges objects
start-method | List of Ranges
start-method | Rle objects
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
strsplitAsListOfIntegerVectors | Low-level string utilities
sub-method | Lists of Atomic Vectors in Natural and Rle Form
sub-method | Rle objects
subject | Views objects
subject-method | List of RleViews
subject-method | Views objects
subjectHits | Set of hits between 2 vector-like objects
subjectHits-method | Set of hits between 2 vector-like objects
subjectHits-method | List of Hits objects
subjectHits-method | Mapping of ranges to another sequence
subjectLength | Set of hits between 2 vector-like objects
subjectLength-method | Set of hits between 2 vector-like objects
subseq | XVector objects
subseq-method | XVector objects
subseq-method | XVectorList objects
subseq<- | XVector objects
subseq<--method | XVector objects
subset-method | The DataTable API
subset-method | Vector objects
subsetByFilter | Collection of Filter Rules
subsetByFilter-method | Collection of Filter Rules
subsetByOverlaps | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
subsetByOverlaps-method | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
substr-method | Rle objects
substring-method | Rle objects
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 | Utility functions and numeric summary of Views of numerics
Summary-method | Lists of Atomic Vectors in Natural and Rle Form
Summary-method | Rle objects
Summary-method | Utility functions and numeric summary of Views of numerics
summary-method | Collection of Filter Rules
summary-method | List of IRanges and NormalIRanges
summary-method | Rle objects
svn.time | Low-level string utilities

## -- T --

t-method | Set of hits between 2 vector-like objects
t-method | List of Hits objects
table-method | Lists of Atomic Vectors in Natural and Rle Form
table-method | Rle objects
tail-method | The DataTable API
tail-method | Vector objects
tapply-method | Vector objects
threebands | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
threebands-method | Intra range transformations of a Ranges, Views, RangesList, MaskCollection, or XVectorList object
tofactor | Grouping 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
tolower-method | Rle objects
toupper-method | Lists of Atomic Vectors in Natural and Rle Form
toupper-method | Rle objects
trim | Views objects
trim-method | Views objects
tseqapply | Apply function and cast to Vector

## -- U --

union-method | Set of hits between 2 vector-like objects
union-method | Set operations on IRanges objects
union-method | List of IRanges and NormalIRanges
union-method | RangesList utility functions
unique-method | Lists of Atomic Vectors in Natural and Rle Form
unique-method | The DataTable API
unique-method | Comparing and ordering ranges
unique-method | Rle objects
unique-method | Vector objects
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-method | List of IRanges and NormalIRanges
unlist-method | List objects
unlist-method | Lists of RangedData
unlist-method | Ranges objects
unlist-method | Simple and Compressed List Classes
unlist_list_of_XVectorList | XVectorList objects
unsplit-method | List objects
unsplit_list_of_XVectorList | XVectorList objects
update-method | IRanges and NormalIRanges objects
update-method | Ranges objects
updateObject-method | Update an object of a class defined in IRanges to its current class definition
updateObject-methods | Update an object of a class defined in IRanges to its current class definition

## -- V --

values | Vector objects
values-method | Data on ranges
values-method | Vector objects
values<- | Vector objects
values<--method | Data on ranges
values<--method | Vector objects
var-method | Lists of Atomic Vectors in Natural and Rle Form
var-method | Rle objects
Vector | Vector objects
Vector-class | Vector objects
viewApply | Utility functions and numeric summary of Views of numerics
viewApply-method | Utility functions and numeric summary of Views of numerics
viewMaxs | Utility functions and numeric summary of Views of numerics
viewMaxs-method | Utility functions and numeric summary of Views of numerics
viewMeans | Utility functions and numeric summary of Views of numerics
viewMeans-method | Utility functions and numeric summary of Views of numerics
viewMins | Utility functions and numeric summary of Views of numerics
viewMins-method | Utility functions and numeric summary of Views of numerics
viewRangeMaxs | Utility functions and numeric summary of Views of numerics
viewRangeMaxs-method | Utility functions and numeric summary of Views of numerics
viewRangeMins | Utility functions and numeric summary of Views of numerics
viewRangeMins-method | Utility functions and numeric summary of Views of numerics
Views | Views objects
Views-class | Views objects
Views-method | The RleViews class
Views-method | List of RleViews
Views-method | The XDoubleViews class
Views-method | The XIntegerViews class
Views-utils | Utility functions and numeric summary of Views of numerics
ViewsList | List of Views
ViewsList-class | List of Views
viewSums | Utility functions and numeric summary of Views of numerics
viewSums-method | Utility functions and numeric summary of Views of numerics
viewWhichMaxs | Utility functions and numeric summary of Views of numerics
viewWhichMaxs-method | Utility functions and numeric summary of Views of numerics
viewWhichMins | Utility functions and numeric summary of Views of numerics
viewWhichMins-method | Utility functions and numeric summary of Views of numerics
vmembers | Grouping objects
vmembers-method | Grouping objects

## -- W --

which-method | Lists of Atomic Vectors in Natural and Rle Form
which-method | Rle objects
which.max-method | Lists of Atomic Vectors in Natural and Rle Form
which.max-method | Rle objects
which.max-method | Utility functions and numeric summary of Views of numerics
which.min-method | Lists of Atomic Vectors in Natural and Rle Form
which.min-method | Utility functions and numeric summary of Views of numerics
whichAsIRanges | IRanges utility functions
whichFirstNotNormal | Ranges objects
whichFirstNotNormal-method | List of IRanges and NormalIRanges
whichFirstNotNormal-method | Ranges objects
width | Ranges objects
width-method | Grouping objects
width-method | IRanges and NormalIRanges objects
width-method | List of IRanges and NormalIRanges
width-method | MaskCollection objects
width-method | Data on ranges
width-method | Ranges objects
width-method | List of Ranges
width-method | Rle objects
width-method | Views objects
width-method | List of Views
width-method | XVectorList objects
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 | The DataTable API
window-method | GappedRanges objects
window-method | IRanges and NormalIRanges objects
window-method | Rle objects
window-method | Vector objects
window-method | XVector objects
window-method | XVectorList objects
window<--method | The DataTable API
window<--method | Data on ranges
window<--method | Vector objects
with-method | List objects
within-method | List objects
within-method | Data on ranges

## -- X --

XDouble | XVector objects
XDouble-class | XVector objects
XDoubleViews | The XDoubleViews class
XDoubleViews-class | The XDoubleViews class
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 | XRawList objects
XRawList-class | XRawList objects
xtabs-method | Statistical modeling with DataTable
xvcopy | Object compaction
xvcopy-method | Object compaction
XVector | XVector objects
XVector-class | XVector objects
XVectorList | XVectorList objects
XVectorList-class | XVectorList objects

## -- misc --

!-method | Lists of Atomic Vectors in Natural and Rle Form
!-method | Rle objects
!=-method | Vector objects
$-method | List objects
$<--method | Data on ranges
$<--method | Simple and Compressed List Classes
%in%-method | Lists of Atomic Vectors in Natural and Rle Form
%in%-method | Rle objects
%in%-method | Vector objects
%in%-method | findOverlaps (and related) methods for Ranges, Views, RangesList, ViewsList, and RangedData objects
<-method | Vector objects
<=-method | Comparing and ordering ranges
==-method | Comparing and ordering ranges
==-method | The XDoubleViews class
==-method | The XIntegerViews class
==-method | XVector objects
>-method | Vector objects
>=-method | Vector objects
[-method | External Data Frame
[-method | List of DataFrames
[-method | Collection of Filter Rules
[-method | GappedRanges objects
[-method | Set of hits between 2 vector-like objects
[-method | IRanges and NormalIRanges objects
[-method | List of IRanges and NormalIRanges
[-method | MaskCollection objects
[-method | Data on ranges
[-method | Ranges objects
[-method | List of Ranges
[-method | Rle objects
[-method | Simple and Compressed List Classes
[-method | Vector objects
[-method | Views objects
[-method | XVector objects
[-method | XVectorList objects
[<--method | External Data Frame
[<--method | List of DataFrames
[<--method | IRanges and NormalIRanges objects
[<--method | Data on ranges
[<--method | Rle objects
[<--method | Simple and Compressed List Classes
[<--method | Vector objects
[<--method | XVectorList objects
[[-method | External Data Frame
[[-method | GappedRanges objects
[[-method | Grouping objects
[[-method | List of IRanges and NormalIRanges
[[-method | List objects
[[-method | MaskCollection objects
[[-method | Data on ranges
[[-method | Ranges objects
[[-method | Simple and Compressed List Classes
[[-method | Views objects
[[-method | XVectorList objects
[[<--method | External Data Frame
[[<--method | Collection of Filter Rules
[[<--method | Data on ranges
[[<--method | Simple and Compressed List Classes
[[<--method | XVectorList objects