Infrastructure for manipulating intervals on sequences

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Documentation for package ‘IRanges’ version 2.12.0

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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 Ranges 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 Data on ranges
as.data.frame-method Ranges objects
as.env-method List of DataFrames
as.env-method Data on ranges
as.factor-method Ranges objects
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.matrix-method Lists of Atomic Vectors in Natural and Rle Form
as.matrix-method CompressedHitsList objects
as.matrix-method Ranges 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 CompressedList objects
c-method Memory-efficient representation of integer positions
c-method IRanges and NormalIRanges objects
c-method Data on ranges
c-method Views objects
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:IPos Memory-efficient representation of integer positions
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: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:SimpleGrouping Grouping objects
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: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: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,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 List of Ranges
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
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 a Ranges, Views, RangesList, or MaskCollection object
disjoin-method Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
disjointBins Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
disjointBins-method Inter range transformations of a Ranges, Views, RangesList, 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 Nested Containment List objects
elementNROWS-method Data on ranges
elementNROWS-method Ranges objects
elementNROWS-method Views objects
end-method Grouping objects
end-method Memory-efficient representation of integer positions
end-method List of IRanges and NormalIRanges
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 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
extractROWS-method Memory-efficient representation of integer positions

-- 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 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
from-method CompressedHitsList objects

-- G --

gaps Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
gaps-method Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
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
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, or MaskCollection object
intersect Set operations on Ranges and RangesList objects
intersect-method Common operations on AtomicList objects
intersect-method Set operations on Ranges and RangesList objects
intra-range-methods Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
IPos Memory-efficient representation of integer positions
IPos-class Memory-efficient representation of integer positions
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 a Ranges, Views, RangesList, or MaskCollection object
isDisjoint-method Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
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

-- 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 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 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
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
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 Memory-efficient representation of integer positions
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 Memory-efficient representation of integer positions
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 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 a Ranges, 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 --

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 Ranges and RangesList objects
pgap-method Set operations on Ranges and RangesList objects
pintersect Set operations on Ranges and RangesList objects
pintersect-method Set operations on Ranges and RangesList 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
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 a Ranges, Views, RangesList, or MaskCollection object
promoters-method Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
psetdiff Set operations on Ranges and RangesList objects
psetdiff-method Set operations on Ranges and RangesList objects
punion Set operations on Ranges and RangesList objects
punion-method Set operations on Ranges and RangesList objects

-- Q --

quantile-method Common operations on AtomicList objects

-- R --

range Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
range-method Common operations on AtomicList objects
range-method Inter range transformations of a Ranges, Views, RangesList, 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 Ranges objects
ranges Squeeze the ranges out of a range-based object
Ranges-class Ranges objects
Ranges-comparison Comparing and ordering ranges
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
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
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 a Ranges, Views, RangesList, or MaskCollection object
reduce-method Inter range transformations of a Ranges, Views, RangesList, or MaskCollection object
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
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 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
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 Ranges and RangesList objects
setdiff-method Set operations on Ranges and RangesList objects
setops-methods Set operations on Ranges 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
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 MaskCollection objects
show-method Data on ranges
show-method Ranges objects
show-method List of Ranges
show-method The RleViews class
showAsCell-method Ranges objects
showAsCell-method List of Ranges
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
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
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
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 Ranges objects
slidingWindows-method Ranges 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 List of Ranges
space-method CompressedHitsList objects
space-method Data on ranges
space-method List of 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 Memory-efficient representation of integer positions
start-method IRanges and NormalIRanges objects
start-method List of IRanges and NormalIRanges
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 Common operations on AtomicList objects
subject Views objects
subject-method List of RleViews
subject-method Views objects
subset-method Vector objects (old man page)
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 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
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 Ranges and RangesList objects
union-method Set operations on Ranges and RangesList objects
unique-method 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-method Lists of Atomic Vectors in Natural and Rle Form
unlist-method CompressedList objects
unlist-method List of IRanges and NormalIRanges
unlist-method Ranges objects
unsplit-method 2 methods that should be documented somewhere else
unstrsplit-method Common operations on AtomicList objects
update-method IRanges and NormalIRanges objects
update-method Ranges objects

-- 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 Ranges objects
whichFirstNotNormal-method Ranges objects
whichFirstNotNormal-method List of Ranges
width Ranges objects
width-method Grouping objects
width-method Memory-efficient representation of integer positions
width-method IRanges and NormalIRanges objects
width-method List of IRanges and NormalIRanges
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 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 Data on ranges
[<--method List of DataFrames
[[-method List of DataFrames
[[-method Data on ranges
[[<--method CompressedList objects
[[<--method List of DataFrames
[[<--method Data on ranges