Infrastructure for manipulating intervals on sequences

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Documentation for package ‘IRanges’ version 2.4.8

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

-- B --

breakInChunks IRanges utility functions

-- C --

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

-- D --

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

-- E --

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

-- F --

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

-- G --

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

-- H --

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

-- I --

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

-- L --

lapply-method Lists of Atomic Vectors in Natural and Rle Form
lapply-method CompressedList objects
lapply-method Data on ranges
length-method CompressedList objects
length-method GappedRanges objects
length-method Grouping objects
length-method Interval Search Forests
length-method Interval Search Trees
length-method MaskCollection objects
length-method Nested Containment List objects
length-method Data on ranges
length-method Ranges objects
length-method Views objects
length<--method Grouping objects
LogicalList Lists of Atomic Vectors in Natural and Rle Form
LogicalList-class Lists of Atomic Vectors in Natural and Rle Form
low2high Grouping objects
low2high-method Grouping objects

-- M --

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

-- N --

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

-- O --

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

-- P --

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

-- Q --

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

-- R --

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

-- S --

score-method Data on ranges
score<--method Data on ranges
sd-method Lists of Atomic Vectors in Natural and Rle Form
selfmatch-method Comparing and ordering ranges
setdiff-method Set operations on IRanges and RangesList objects
setops-methods Set operations on IRanges and RangesList objects
shift Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
shift-method Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
shiftApply Vector objects (old man page)
shiftApply-method Vector objects (old man page)
show-method Lists of Atomic Vectors in Natural and Rle Form
show-method List of DataFrames
show-method GappedRanges objects
show-method Grouping objects
show-method Interval Search Forests
show-method MaskCollection objects
show-method Data on ranges
show-method Ranges objects
show-method List of Ranges
show-method The RleViews class
showAsCell-method Lists of Atomic Vectors in Natural and Rle Form
showAsCell-method Ranges objects
showAsCell-method List of Ranges
showAsCell-method Vector objects (old man page)
SimpleAtomicList Lists of Atomic Vectors in Natural and Rle Form
SimpleAtomicList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleDataFrameList-class List of DataFrames
SimpleFactorList Lists of Atomic Vectors in Natural and Rle Form
SimpleFactorList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleIRangesList List of IRanges and NormalIRanges
SimpleIRangesList-class List of IRanges and NormalIRanges
SimpleLogicalList Lists of Atomic Vectors in Natural and Rle Form
SimpleLogicalList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleNormalIRangesList List of IRanges and NormalIRanges
SimpleNormalIRangesList-class List of IRanges and NormalIRanges
SimpleNumericList Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRangesList List of Ranges
SimpleRangesList-class List of Ranges
SimpleRawList Lists of Atomic Vectors in Natural and Rle Form
SimpleRawList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRleViewsList-class List of RleViews
SimpleSplitDataFrameList-class List of DataFrames
SimpleViewsList List of Views
SimpleViewsList-class List of Views
simplify Applying over spaces
simplify-method Applying over spaces
simplify<- Applying over spaces
simplify<--method Applying over spaces
slice Slice a vector-like or list-like object
slice-method Slice a vector-like or list-like object
slice-methods Slice a vector-like or list-like object
smoothEnds-method Lists of Atomic Vectors in Natural and Rle Form
solveUserSEW The IRanges constructor and supporting functions
solveUserSEW0 The IRanges constructor and supporting functions
sort-method Lists of Atomic Vectors in Natural and Rle Form
sort.List Lists of Atomic Vectors in Natural and Rle Form
space List of Ranges
space-method List of Hits objects
space-method Data on ranges
space-method List of Ranges
split-method Data on ranges
split<--method 2 methods that should be documented somewhere else
splitAsList Group elements of a vector-like object into a list-like object
splitAsList,ANY,List Group elements of a vector-like object into a list-like object
splitAsList,ANY,Rle Group elements of a vector-like object into a list-like object
splitAsList,ANY,vectorORfactor Group elements of a vector-like object into a list-like object
SplitDataFrameList List of DataFrames
SplitDataFrameList-class List of DataFrames
splitRanges Rle objects (old man page)
splitRanges-method Rle objects (old man page)
stack-method List of DataFrames
stack-method List objects (old man page)
stack-method Lists of RangedData
start-method GappedRanges objects
start-method Grouping objects
start-method IRanges and NormalIRanges objects
start-method List of IRanges and NormalIRanges
start-method Interval Search Forests
start-method Interval Search Trees
start-method Nested Containment List objects
start-method Data on ranges
start-method Ranges objects
start-method List of Ranges
start-method Views objects
start-method List of Views
start<- Ranges objects
start<--method IRanges and NormalIRanges objects
start<--method Data on ranges
start<--method List of Ranges
start<--method Views objects
sub-method Lists of Atomic Vectors in Natural and Rle Form
subject Views objects
subject-method List of RleViews
subject-method Views objects
subjectHits-method List of Hits objects
subjectLength-method List of Hits objects
subset-method Vector objects (old man page)
subsetByOverlaps Finding overlapping ranges
subsetByOverlaps-method Finding overlapping ranges
subviews Views objects
subviews-method Views objects
successiveIRanges IRanges utility functions
successiveViews Views objects
sum-method Lists of Atomic Vectors in Natural and Rle Form
sum-method Summarize views on a vector-like object with numeric values
Summary-method Lists of Atomic Vectors in Natural and Rle Form
Summary-method Summarize views on a vector-like object with numeric values
summary-method List of IRanges and NormalIRanges

-- T --

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

-- U --

union-method Set operations on IRanges and RangesList objects
unique-method Lists of Atomic Vectors in Natural and Rle Form
unique.CompressedList Lists of Atomic Vectors in Natural and Rle Form
unique.RleList Lists of Atomic Vectors in Natural and Rle Form
universe List of Ranges
universe-method Data on ranges
universe-method List of Ranges
universe-method List of Views
universe<- List of Ranges
universe<--method Data on ranges
universe<--method List of Ranges
universe<--method List of Views
unlist,SimpleFactorList Lists of Atomic Vectors in Natural and Rle Form
unlist,SimpleRleList Lists of Atomic Vectors in Natural and Rle Form
unlist-method CompressedList objects
unlist-method List of IRanges and NormalIRanges
unlist-method Lists of RangedData
unlist-method Ranges objects
unsplit-method 2 methods that should be documented somewhere else
unstrsplit-method Lists of Atomic Vectors in Natural and Rle Form
update-method IRanges and NormalIRanges objects
update-method Ranges objects
updateObject-method Update an object of a class defined in the IRanges package to its current class definition
updateObject-methods Update an object of a class defined in the IRanges package to its current class definition

-- V --

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

-- W --

which-method Lists of Atomic Vectors in Natural and Rle Form
which.max-method Lists of Atomic Vectors in Natural and Rle Form
which.max-method Summarize views on a vector-like object with numeric values
which.min-method Lists of Atomic Vectors in Natural and Rle Form
which.min-method Summarize views on a vector-like object with numeric values
whichAsIRanges IRanges utility functions
whichFirstNotNormal Ranges objects
whichFirstNotNormal-method Ranges objects
whichFirstNotNormal-method List of Ranges
width Ranges objects
width-method Grouping objects
width-method IRanges and NormalIRanges objects
width-method List of IRanges and NormalIRanges
width-method Interval Search Forests
width-method MaskCollection objects
width-method Nested Containment List objects
width-method Data on ranges
width-method Ranges objects
width-method List of Ranges
width-method Views objects
width-method List of Views
width<- Ranges objects
width<--method IRanges and NormalIRanges objects
width<--method Data on ranges
width<--method List of Ranges
width<--method Views objects
window<--method 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 Interval Search Forests
[-method Data on ranges
[<--method List of DataFrames
[[-method List of DataFrames
[[-method Data on ranges
[[<--method CompressedList objects
[[<--method List of DataFrames
[[<--method Data on ranges