# Infrastructure for manipulating intervals on sequences

## Documentation for package ‘IRanges’ version 2.14.12

- 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 | MaskCollection objects
active<- | MaskCollection objects
active<--method | MaskCollection objects
all-method | Common operations on AtomicList objects
any-method | Common operations on AtomicList objects
anyNA-method | Common operations on AtomicList objects
append-method | MaskCollection objects
as.character-method | IPosRanges objects
as.data.frame-method | Examples of basic manipulation of Hits objects
as.data.frame-method | Memory-efficient representation of integer positions
as.data.frame-method | IPosRanges objects
as.data.frame-method | Data on ranges
as.env-method | List of DataFrames
as.env-method | Data on ranges
as.factor-method | IPosRanges 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.matrix-method | Lists of Atomic Vectors in Natural and Rle Form
as.matrix-method | CompressedHitsList objects
as.matrix-method | IPosRanges objects
as.matrix-method | Views objects
as.matrix-method | List of Views
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
AtomicList-utils | Common operations on AtomicList objects

## -- B --

breakInChunks | IRanges utility functions

## -- C --

c-method | Data on ranges
cbind-method | List of DataFrames
CharacterList | Lists of Atomic Vectors in Natural and Rle Form
CharacterList-class | Lists of Atomic Vectors in Natural and Rle Form
chartr-method | Common operations on AtomicList objects
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:CompressedGrouping | Grouping objects
class:CompressedHitsList | CompressedHitsList 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:CompressedManyToManyGrouping | Grouping objects
class:CompressedManyToOneGrouping | Grouping objects
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:Grouping | Grouping objects
class:GroupingIRanges | Grouping objects
class:GroupingRanges | Grouping objects
class:H2LGrouping | Grouping objects
class:IntegerList | Lists of Atomic Vectors in Natural and Rle Form
class:IntegerRanges | IntegerRanges objects
class:IntegerRangesList-class | IntegerRangesList objects
class:IntegerRanges_OR_missing | Finding the nearest range neighbor
class:IPos | Memory-efficient representation of integer positions
class:IPosRanges | IPosRanges objects
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:ManyToManyGrouping | Grouping objects
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: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:SimpleGrouping | Grouping objects
class:SimpleIntegerList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleIntegerRangesList-class | IntegerRangesList objects
class:SimpleIRangesList | List of IRanges and NormalIRanges
class:SimpleLogicalList | Lists of Atomic Vectors in Natural and Rle Form
class:SimpleManyToManyGrouping | Grouping objects
class:SimpleManyToOneGrouping | Grouping objects
class:SimpleNormalIRangesList | List of IRanges and NormalIRanges
class:SimpleNumericList | Lists of Atomic Vectors in Natural and Rle Form
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,AtomicList,RleViews | Lists of Atomic Vectors in Natural and Rle Form
coerce,Hits,Grouping | Examples of basic manipulation of Hits objects
coerce-method | Lists of Atomic Vectors in Natural and Rle Form
coerce-method | CompressedList objects
coerce-method | List of DataFrames
coerce-method | Grouping objects
coerce-method | Examples of basic manipulation of Hits objects
coerce-method | Memory-efficient representation of integer positions
coerce-method | IRanges and NormalIRanges objects
coerce-method | IRanges utility functions
coerce-method | List of IRanges and NormalIRanges
coerce-method | MaskCollection objects
coerce-method | Nested Containment List objects
coerce-method | Data on ranges
coerce-method | Selection of ranges and columns
coerce-method | Rle objects (old man page)
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
Complex-method | Common operations on AtomicList objects
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
CompressedGrouping-class | Grouping objects
CompressedHitsList | CompressedHitsList objects
CompressedHitsList-class | CompressedHitsList 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
CompressedManyToManyGrouping-class | Grouping objects
CompressedManyToOneGrouping-class | Grouping objects
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
concatenateObjects-method | CompressedList objects
concatenateObjects-method | Grouping objects
concatenateObjects-method | Memory-efficient representation of integer positions
concatenateObjects-method | Nested Containment List objects
concatenateObjects-method | Views objects
cor-method | Common operations on AtomicList objects
countOverlaps | Finding overlapping ranges
countOverlaps-method | Finding overlapping ranges
cov-method | Common operations on AtomicList objects
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 | Common operations on AtomicList objects
cummin-method | Common operations on AtomicList objects
cumprod-method | Common operations on AtomicList objects
cumsum-method | Common operations on AtomicList objects

## -- 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 | Common operations on AtomicList objects
diff.AtomicList | Common operations on AtomicList objects
dim-method | List of DataFrames
dimnames-method | List of DataFrames
dimnames<--method | List of DataFrames
disjoin | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjoin-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjointBins | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjointBins-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection 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
Dups | Grouping objects
Dups-class | Grouping objects

## -- E --

elementNROWS-method | CompressedList objects
elementNROWS-method | IPosRanges objects
elementNROWS-method | Nested Containment List objects
elementNROWS-method | Data on ranges
end-method | Grouping objects
end-method | IPosRanges objects
end-method | List of IRanges and NormalIRanges
end-method | IntegerRangesList objects
end-method | Nested Containment List objects
end-method | Data on ranges
end-method | List of Views
end<- | IPosRanges objects
end<--method | IRanges and NormalIRanges objects
end<--method | IntegerRangesList objects
end<--method | Data on ranges
end<--method | Views objects
equisplit | Extract list fragments from a list-like object
eval | Vector objects (old man page)
eval-method | Vector objects (old man page)
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
extractListFragments | Extract list fragments from a list-like object
extractROWS-method | Grouping objects
extractROWS-method | Memory-efficient representation of integer positions
extractROWS-method | Nested Containment List objects

## -- F --

FactorList | Lists of Atomic Vectors in Natural and Rle Form
FactorList-class | Lists of Atomic Vectors in Natural and Rle Form
findOverlapPairs | Finding overlapping ranges
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 an IRanges, IPos, Views, RangesList, or MaskCollection object
flank-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
follow | Finding the nearest range neighbor
follow-method | Finding the nearest range neighbor
from-method | CompressedHitsList objects

## -- G --

gaps | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
gaps-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
getListElement-method | IPosRanges objects
Grouping | Grouping objects
Grouping-class | Grouping objects
GroupingIRanges | Grouping objects
GroupingIRanges-class | Grouping objects
GroupingRanges | Grouping objects
GroupingRanges-class | Grouping objects
grouplengths | Grouping objects
grouplengths-method | Grouping objects
grouprank | Grouping objects
grouprank-method | Grouping objects
gsub-method | Common operations on AtomicList objects

## -- H --

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

## -- I --

ifelse2 | Common operations on AtomicList objects
ifelse2-method | Common operations on AtomicList objects
INCOMPATIBLE_ARANGES_MSG | Extract list fragments from a list-like object
IntegerList | Lists of Atomic Vectors in Natural and Rle Form
IntegerList-class | Lists of Atomic Vectors in Natural and Rle Form
IntegerRanges | IntegerRanges objects
IntegerRanges-class | IntegerRanges objects
IntegerRangesList | IntegerRangesList objects
IntegerRangesList-class | IntegerRangesList objects
IntegerRanges_OR_missing | Finding the nearest range neighbor
IntegerRanges_OR_missing-class | Finding the nearest range neighbor
inter-range-methods | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
intersect | Set operations on IntegerRanges and IntegerRangesList objects
intersect-method | Common operations on AtomicList objects
intersect-method | Set operations on IntegerRanges and IntegerRangesList objects
intra-range-methods | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
IPos | Memory-efficient representation of integer positions
IPos-class | Memory-efficient representation of integer positions
IPosRanges | IPosRanges objects
IPosRanges-class | IPosRanges objects
IPosRanges-comparison | Comparing and ordering ranges
IQR-method | Common operations on AtomicList objects
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
is.na-method | CompressedList objects
is.unsorted-method | Comparing and ordering ranges
isDisjoint | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
isDisjoint-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
isEmpty-method | IPosRanges objects
isEmpty-method | IRanges and NormalIRanges objects
isNormal | IPosRanges objects
isNormal-method | IPosRanges objects
isNormal-method | IRanges and NormalIRanges objects
isNormal-method | List of IRanges and NormalIRanges
isNormal-method | IntegerRangesList objects

## -- 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 | Grouping objects
length-method | Memory-efficient representation of integer positions
length-method | IPosRanges objects
length-method | MaskCollection objects
length-method | Nested Containment List objects
length-method | Data on ranges
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 | Common operations on AtomicList objects
ManyToManyGrouping | Grouping objects
ManyToManyGrouping-class | Grouping objects
ManyToOneGrouping | Grouping objects
ManyToOneGrouping-class | Grouping objects
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 | CompressedList objects
match-method | Comparing and ordering ranges
Math-method | Common operations on AtomicList objects
Math2-method | Common operations on AtomicList objects
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 | Common operations on AtomicList objects
mean-method | Summarize views on a vector-like object with numeric values
median-method | Common operations on AtomicList objects
members | Grouping objects
members-method | Grouping objects
merge-method | IntegerRangesList objects
mergeByOverlaps | Finding overlapping ranges
mid | IPosRanges objects
mid-method | IPosRanges 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
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 | Grouping objects
names-method | IPosRanges objects
names-method | IRanges and NormalIRanges objects
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 | Grouping objects
names<--method | IPosRanges 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 an IRanges, IPos, Views, RangesList, or MaskCollection object
narrow-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
nchar-method | Common operations on AtomicList objects
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
nir_list | MaskCollection objects
nir_list-method | MaskCollection objects
nLnode-method | CompressedHitsList 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
nRnode-method | CompressedHitsList objects
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 | Common operations on AtomicList objects
Ops-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
order-method | Lists of Atomic Vectors in Natural and Rle Form
order-method | Common operations on AtomicList objects
order-method | Comparing and ordering ranges
overlapsAny | Finding overlapping ranges
overlapsAny-method | Finding overlapping ranges
overlapsRanges | Finding overlapping ranges
overlapsRanges-method | Finding overlapping ranges

## -- P --

parallelSlotNames-method | Grouping objects
parallelSlotNames-method | IRanges and NormalIRanges objects
parallelSlotNames-method | Nested Containment List objects
parallelSlotNames-method | Views objects
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
paste-method | Common operations on AtomicList objects
pcompare | Comparing and ordering ranges
pcompare-method | Comparing and ordering ranges
pgap | Set operations on IntegerRanges and IntegerRangesList objects
pgap-method | Set operations on IntegerRanges and IntegerRangesList objects
pintersect | Set operations on IntegerRanges and IntegerRangesList objects
pintersect-method | Set operations on IntegerRanges and IntegerRangesList objects
pmax-method | Common operations on AtomicList objects
pmax.int-method | Common operations on AtomicList objects
pmin-method | Common operations on AtomicList objects
pmin.int-method | Common operations on AtomicList objects
pos | Memory-efficient representation of integer positions
pos-method | Memory-efficient representation of integer positions
pos-method | List of IRanges and NormalIRanges
pos-method | IntegerRangesList objects
poverlaps | Finding overlapping ranges
poverlaps-method | Finding overlapping ranges
precede | Finding the nearest range neighbor
precede-method | Finding the nearest range neighbor
promoters | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
promoters-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
psetdiff | Set operations on IntegerRanges and IntegerRangesList objects
psetdiff-method | Set operations on IntegerRanges and IntegerRangesList objects
punion | Set operations on IntegerRanges and IntegerRangesList objects
punion-method | Set operations on IntegerRanges and IntegerRangesList objects

## -- Q --

quantile-method | Common operations on AtomicList objects

## -- R --

range | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
range-method | Common operations on AtomicList objects
range-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
range-squeezers | Squeeze the ranges out of a range-based object
rangeComparisonCodeToLetter | Comparing and ordering ranges
RangedData | Data on ranges
RangedData-class | Data on ranges
RangedSelection | Selection of ranges and columns
RangedSelection-class | Selection of ranges and columns
ranges | Squeeze the ranges out of a range-based object
ranges-method | Lists of Atomic Vectors in Natural and Rle Form
ranges-method | IRanges and NormalIRanges 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
rank-method | Lists of Atomic Vectors in Natural and Rle Form
rank-method | Common operations on AtomicList objects
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 | Data on ranges
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 an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
reduce-method | Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
reflect | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
reflect-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
regroup | Group elements of a vector-like object into a list-like object
relist-method | Group elements of a vector-like object into a list-like object
relistToClass-method | Common operations on DataFrame objects
rep-method | Vector objects (old man page)
rep.int-method | Vector objects (old man page)
resize | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
resize-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
restrict | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
restrict-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
rev-method | Vector objects (old man page)
revElements-method | CompressedList objects
reverse | reverse
reverse-method | reverse
rglist | Squeeze the ranges out of a range-based object
rglist-method | Squeeze the ranges out of a range-based object
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 | Common operations on AtomicList objects
runmed-method | Common operations on AtomicList objects
runq-method | Common operations on AtomicList objects
runsum-method | Common operations on AtomicList objects
runValue-method | Lists of Atomic Vectors in Natural and Rle Form
runValue<--method | Lists of Atomic Vectors in Natural and Rle Form
runwtsum-method | Common operations on AtomicList objects

## -- S --

score-method | Data on ranges
score<--method | Data on ranges
sd-method | Common operations on AtomicList objects
selectNearest | Finding the nearest range neighbor
selfmatch-method | Common operations on AtomicList objects
selfmatch-method | Comparing and ordering ranges
setdiff | Set operations on IntegerRanges and IntegerRangesList objects
setdiff-method | Set operations on IntegerRanges and IntegerRangesList objects
setops-methods | Set operations on IntegerRanges and IntegerRangesList objects
shift | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
shift-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
show-method | Lists of Atomic Vectors in Natural and Rle Form
show-method | List of DataFrames
show-method | Grouping objects
show-method | Memory-efficient representation of integer positions
show-method | IPosRanges objects
show-method | IntegerRangesList objects
show-method | MaskCollection objects
show-method | Data on ranges
show-method | The RleViews class
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
SimpleGrouping-class | Grouping objects
SimpleIntegerList | Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class | Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerRangesList | IntegerRangesList objects
SimpleIntegerRangesList-class | IntegerRangesList objects
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
SimpleManyToManyGrouping-class | Grouping objects
SimpleManyToOneGrouping-class | Grouping objects
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
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
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
slidingWindows | IPosRanges objects
slidingWindows-method | IPosRanges objects
smoothEnds-method | Common operations on AtomicList 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
space | IntegerRangesList objects
space-method | CompressedHitsList objects
space-method | IntegerRangesList objects
space-method | Data on ranges
split<--method | 2 methods that should be documented somewhere else
splitAsList | Group elements of a vector-like object into a list-like object
splitAsList,ANY,ANY | 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)
start-method | Grouping objects
start-method | IPosRanges objects
start-method | IRanges and NormalIRanges objects
start-method | List of IRanges and NormalIRanges
start-method | IntegerRangesList objects
start-method | Nested Containment List objects
start-method | Data on ranges
start-method | Views objects
start-method | List of Views
start<- | IPosRanges objects
start<--method | IRanges and NormalIRanges objects
start<--method | IntegerRangesList objects
start<--method | Data on ranges
start<--method | Views objects
sub-method | Common operations on AtomicList objects
subject | Views objects
subject-method | List of RleViews
subject-method | Views objects
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 | Common operations on AtomicList objects
sum-method | Summarize views on a vector-like object with numeric values
Summary-method | Common operations on AtomicList objects
Summary-method | Summarize views on a vector-like object with numeric values
summary-method | List of IRanges and NormalIRanges

## -- T --

table-method | Lists of Atomic Vectors in Natural and Rle Form
tapply-method | Vector objects (old man page)
threebands | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
threebands-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
tile | IPosRanges objects
tile-method | IPosRanges objects
to-method | CompressedHitsList objects
togroup | Grouping objects
togroup-method | Grouping objects
togrouplength | Grouping objects
togrouplength-method | Grouping objects
togrouprank | Grouping objects
togrouprank-method | Grouping objects
tolower-method | Common operations on AtomicList objects
toupper-method | Common operations on AtomicList objects
transform-method | List of DataFrames
trim | Views objects
trim-method | Views objects

## -- U --

union | Set operations on IntegerRanges and IntegerRangesList objects
union-method | Set operations on IntegerRanges and IntegerRangesList objects
unique-method | Lists of Atomic Vectors in Natural and Rle Form
universe | IntegerRangesList objects
universe-method | IntegerRangesList objects
universe-method | Data on ranges
universe-method | List of Views
universe<- | IntegerRangesList objects
universe<--method | IntegerRangesList objects
universe<--method | Data on ranges
universe<--method | List of Views
unlist-method | Lists of Atomic Vectors in Natural and Rle Form
unlist-method | CompressedList objects
unlist-method | List of IRanges and NormalIRanges
unlist-method | Views objects
unsplit-method | 2 methods that should be documented somewhere else
unstrsplit-method | Common operations on AtomicList objects
update_ranges | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
update_ranges-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object

## -- V --

values-method | Data on ranges
values<--method | Data on ranges
var-method | Common operations on AtomicList objects
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 | Common operations on AtomicList objects
which.max-method | Common operations on AtomicList objects
which.max-method | Summarize views on a vector-like object with numeric values
which.min-method | Common operations on AtomicList objects
which.min-method | Summarize views on a vector-like object with numeric values
whichAsIRanges | IRanges utility functions
whichFirstNotNormal | IPosRanges objects
whichFirstNotNormal-method | IPosRanges objects
whichFirstNotNormal-method | IntegerRangesList objects
width | IPosRanges objects
width-method | Grouping objects
width-method | IPosRanges objects
width-method | IRanges and NormalIRanges objects
width-method | List of IRanges and NormalIRanges
width-method | IntegerRangesList objects
width-method | MaskCollection objects
width-method | Nested Containment List objects
width-method | Data on ranges
width-method | Views objects
width-method | List of Views
width<- | IPosRanges objects
width<--method | IRanges and NormalIRanges objects
width<--method | IntegerRangesList objects
width<--method | Data on ranges
width<--method | Views objects
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)
windows-method | Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
with-method | Vector objects (old man page)
within-method | Data on ranges

## -- misc --

!-method | CompressedList objects
%outside% | Finding overlapping ranges
%over% | Finding overlapping ranges
%within% | Finding overlapping ranges
[-method | List of DataFrames
[-method | Data on ranges
[<--method | List of DataFrames
[[-method | List of DataFrames
[[-method | Data on ranges
[[<--method | List of DataFrames
[[<--method | Data on ranges