Infrastructure for manipulating intervals on sequences

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Documentation for package ‘IRanges’ version 1.22.10

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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 X misc

-- A --

active MaskCollection objects
active-method Collection of Filter Rules
active-method MaskCollection objects
active<- MaskCollection objects
active<--method Collection of Filter Rules
active<--method MaskCollection objects
aggregate-method External Data Frame
aggregate-method The DataTable API
aggregate-method Rle objects
aggregate-method Simple and Compressed List Classes
aggregate-method Vector objects
aggregate.Rle Rle objects
all-method Lists of Atomic Vectors in Natural and Rle Form
Annotated Annotated class
Annotated-class Annotated class
append-method Collection of Filter Rules
append-method MaskCollection objects
append-method Vector objects
applyFun Applying over spaces
applyFun-method Applying over spaces
applyFun<- Applying over spaces
applyFun<--method Applying over spaces
applyParams Applying over spaces
applyParams-method Applying over spaces
applyParams<- Applying over spaces
applyParams<--method Applying over spaces
as.character-method Rle objects
as.character-method Vector objects
as.complex-method Rle objects
as.complex-method Vector objects
as.data.frame-method External Data Frame
as.data.frame-method List of DataFrames
as.data.frame-method GappedRanges objects
as.data.frame-method Set of hits between 2 vector-like objects
as.data.frame-method Data on ranges
as.data.frame-method Ranges objects
as.data.frame-method List of Ranges
as.data.frame-method Rle objects
as.data.frame-method Vector objects
as.data.frame.DataFrame External Data Frame
as.data.frame.DataFrameList List of DataFrames
as.data.frame.GappedRanges GappedRanges objects
as.data.frame.Hits Set of hits between 2 vector-like objects
as.data.frame.RangedData Data on ranges
as.data.frame.Ranges Ranges objects
as.data.frame.RangesList List of Ranges
as.data.frame.Rle Rle objects
as.data.frame.Vector Vector objects
as.double-method Vector objects
as.env List objects
as.env-method The DataTable API
as.env-method List objects
as.env-method Data on ranges
as.env-method Vector objects
as.factor-method Rle objects
as.integer-method Ranges objects
as.integer-method Rle objects
as.integer-method Vector objects
as.list-method Lists of Atomic Vectors in Natural and Rle Form
as.list-method Set of hits between 2 vector-like objects
as.list-method List of IRanges and NormalIRanges
as.list-method List objects
as.list-method Rle objects
as.list-method Simple and Compressed List Classes
as.list.CompressedNormalIRangesList List of IRanges and NormalIRanges
as.list.Hits Set of hits between 2 vector-like objects
as.list.List List objects
as.list.Rle Rle objects
as.list.SimpleList Simple and Compressed List Classes
as.logical-method Rle objects
as.logical-method Vector objects
as.matrix-method External Data Frame
as.matrix-method Set of hits between 2 vector-like objects
as.matrix-method List of Hits objects
as.matrix-method Ranges objects
as.matrix-method Views objects
as.matrix-method List of Views
as.numeric-method Rle objects
as.numeric-method Vector objects
as.raw-method Rle objects
as.raw-method Vector objects
as.table-method Set of hits between 2 vector-like objects
as.table-method List of Hits objects
as.vector-method Lists of Atomic Vectors in Natural and Rle Form
as.vector-method Rle objects
as.vectorORfactor Rle objects
as.vectorORfactor-method Rle objects
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
by-method The DataTable API

-- C --

c-method Collection of Filter Rules
c-method GappedRanges objects
c-method IRanges and NormalIRanges objects
c-method Data on ranges
c-method Rle objects
c-method Simple and Compressed List Classes
c-method Vector objects
c-method Views objects
cbind-method External Data Frame
cbind-method List of DataFrames
cbind-method The DataTable API
cbind-method Matrix for Filter Results
CharacterList Lists of Atomic Vectors in Natural and Rle Form
CharacterList-class Lists of Atomic Vectors in Natural and Rle Form
chartr-method Lists of Atomic Vectors in Natural and Rle Form
chartr-method Rle 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:CompressedIntegerList Lists of Atomic Vectors in Natural and Rle Form
class:CompressedIRangesList List of IRanges and NormalIRanges
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:DataFrame External Data Frame
class:DataTable The DataTable API
class:DataTableORNULL The DataTable API
class:Dups Grouping objects
class:GappedRanges GappedRanges objects
class:Grouping Grouping objects
class:H2LGrouping Grouping 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:List List objects
class:LogicalList Lists of Atomic Vectors in Natural and Rle Form
class:MaskCollection MaskCollection 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: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:Rle Rle objects
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: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:Vector Vector objects
class:Views Views objects
class:ViewsList List of Views
classNameForDisplay Provide a class name for displaying to users
classNameForDisplay-method Provide a class name for displaying to users
coerce-method Lists of Atomic Vectors in Natural and Rle Form
coerce-method External Data Frame
coerce-method List of DataFrames
coerce-method GappedRanges objects
coerce-method Grouping objects
coerce-method Set of hits between 2 vector-like objects
coerce-method IRanges and NormalIRanges objects
coerce-method IRanges utility functions
coerce-method List of IRanges and NormalIRanges
coerce-method Interval Search Forests
coerce-method Interval Search Trees
coerce-method List objects
coerce-method MaskCollection objects
coerce-method Data on ranges
coerce-method Selection of ranges and columns
coerce-method List of Ranges
coerce-method Mapping of ranges to another sequence
coerce-method Rle objects
coerce-method The RleViews class
coerce-method List of RleViews
coerce-method Simple and Compressed List Classes
coerce-method Vector objects
coerce-method Views objects
collapse MaskCollection objects
collapse-method MaskCollection objects
colnames-method External Data Frame
colnames-method List of DataFrames
colnames-method Data on ranges
colnames-method Selection of ranges and columns
colnames<--method External Data Frame
colnames<--method List of DataFrames
colnames<--method Data on ranges
colnames<--method Selection of ranges and columns
columnMetadata List of DataFrames
columnMetadata-method List of DataFrames
columnMetadata-method Data on ranges
columnMetadata<- List of DataFrames
columnMetadata<--method List of DataFrames
columnMetadata<--method Data on ranges
compare Compare, order, tabulate vector-like objects
compare-method Comparing and ordering ranges
complete.cases-method The DataTable API
Complex-method Lists of Atomic Vectors in Natural and Rle Form
Complex-method Rle objects
ComplexList Lists of Atomic Vectors in Natural and Rle Form
ComplexList-class Lists of Atomic Vectors in Natural and Rle Form
CompressedAtomicList 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
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 Simple and Compressed List Classes
CompressedList-class Simple and Compressed List Classes
CompressedLogicalList Lists of Atomic Vectors in Natural and Rle Form
CompressedLogicalList-class Lists of Atomic Vectors in Natural and Rle Form
CompressedNormalIRangesList List of IRanges and NormalIRanges
CompressedNormalIRangesList-class List of IRanges and NormalIRanges
CompressedNumericList Lists of Atomic Vectors in Natural and Rle Form
CompressedNumericList-class Lists of Atomic Vectors in Natural and Rle Form
CompressedRawList Lists of Atomic Vectors in Natural and Rle Form
CompressedRawList-class Lists of Atomic Vectors in Natural and Rle Form
CompressedRleList Lists of Atomic Vectors in Natural and Rle Form
CompressedRleList-class Lists of Atomic Vectors in Natural and Rle Form
CompressedSplitDataFrameList-class List of DataFrames
cor-method Lists of Atomic Vectors in Natural and Rle Form
cor-method Rle objects
countMatches Compare, order, tabulate vector-like objects
countMatches-method Compare, order, tabulate vector-like objects
countOverlaps Finding overlapping ranges
countOverlaps-method Finding overlapping ranges
countQueryHits Set of hits between 2 vector-like objects
countQueryHits-method Set of hits between 2 vector-like objects
countSubjectHits Set of hits between 2 vector-like objects
countSubjectHits-method Set of hits between 2 vector-like objects
cov-method Lists of Atomic Vectors in Natural and Rle Form
cov-method Rle objects
coverage Coverage 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 External Data Frame
DataFrame-class External Data Frame
DataFrameList List of DataFrames
DataFrameList-class List of DataFrames
DataTable The DataTable API
DataTable-API The DataTable API
DataTable-class The DataTable API
DataTable-stats Statistical modeling with DataTable
DataTableORNULL The DataTable API
DataTableORNULL-class The DataTable API
desc MaskCollection objects
desc-method MaskCollection objects
desc<- MaskCollection objects
desc<--method MaskCollection objects
diff-method Lists of Atomic Vectors in Natural and Rle Form
diff-method Rle objects
diff.Rle Rle objects
dim-method List of DataFrames
dim-method The DataTable API
dim-method Mapping of ranges to another sequence
dimnames-method List of DataFrames
dimnames-method The DataTable API
dimnames<--method List of DataFrames
dimnames<--method The DataTable API
disjoin Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjoin-method Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjointBins Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
disjointBins-method Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
distance Finding the nearest range neighbor
distance-method Finding the nearest range neighbor
distanceToNearest Finding the nearest range neighbor
distanceToNearest-method Finding the nearest range neighbor
drop-method Lists of Atomic Vectors in Natural and Rle Form
duplicated-method The DataTable API
duplicated-method Grouping objects
duplicated-method Rle objects
duplicated-method Compare, order, tabulate vector-like objects
duplicated.DataTable The DataTable API
duplicated.Dups Grouping objects
duplicated.Rle Rle objects
duplicated.Vector Compare, order, tabulate vector-like objects
Dups Grouping objects
Dups-class Grouping objects

-- E --

elementLengths List objects
elementLengths-method GappedRanges objects
elementLengths-method Interval Search Forests
elementLengths-method List objects
elementLengths-method Data on ranges
elementLengths-method Ranges objects
elementLengths-method Views objects
elementMetadata Vector objects
elementMetadata-method Vector objects
elementMetadata<- Vector objects
elementMetadata<--method Vector objects
elementType List objects
elementType-method List objects
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 Data on ranges
end-method Ranges objects
end-method List of Ranges
end-method Rle objects
end-method Views objects
end-method List of Views
end<- Ranges objects
end<--method IRanges and NormalIRanges objects
end<--method Data on ranges
end<--method List of Ranges
end<--method Views objects
endoapply Endomorphisms via application of a function over an object's elements
endoapply-method List objects
endoapply-method Data on ranges
endoapply-method Simple and Compressed List Classes
endoapply-method Endomorphisms via application of a function over an object's elements
eval List objects
eval-method Collection of Filter Rules
eval-method List objects
eval-method Vector objects
evalSeparately Collection of Filter Rules
evalSeparately-method Collection of Filter Rules
expand The expand method for uncompressing compressed data columns
expand-method The expand method for uncompressing compressed data columns
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 --

Filter-method Functional programming methods for List objects
FilterMatrix Matrix for Filter Results
FilterMatrix-class Matrix for Filter Results
FilterRules Collection of Filter Rules
filterRules Applying over spaces
FilterRules-class Collection of Filter Rules
filterRules-method Matrix for Filter Results
filterRules-method Applying over spaces
filterRules<- Applying over spaces
filterRules<--method Applying over spaces
Find-method Functional programming methods for List objects
findMatches Compare, order, tabulate vector-like objects
findMatches-method Compare, order, tabulate vector-like objects
findOverlaps Finding overlapping ranges
findOverlaps-method Finding overlapping ranges
findOverlaps-methods Finding overlapping ranges
findRange Rle objects
findRange-method Rle objects
findRun Rle objects
findRun-method Rle objects
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
funprog-methods Functional programming methods for List objects

-- G --

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

-- H --

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

-- I --

ifelse-method Rle objects
IntegerList Lists of Atomic Vectors in Natural and Rle Form
IntegerList-class Lists of Atomic Vectors in Natural and Rle Form
inter-range-methods Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
intersect-method Rle objects
intersect-method Set operations on IRanges, RangesList, and Hits 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
IQR-method Rle objects
IRanges The IRanges constructor and supporting functions
IRanges-class IRanges and NormalIRanges objects
IRanges-constructor The IRanges constructor and supporting functions
IRanges-utils IRanges utility functions
IRangesList List of IRanges and NormalIRanges
IRangesList-class List of IRanges and NormalIRanges
is.na-method The DataTable API
is.na-method Rle objects
is.unsorted-method Rle objects
isConstant Test if an atomic vector or array is constant
isConstant-method Test if an atomic vector or array is constant
isDisjoint Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
isDisjoint-method Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
isEmpty List objects
isEmpty-method IRanges and NormalIRanges objects
isEmpty-method List objects
isEmpty-method Ranges objects
isEmpty-method Simple and Compressed List Classes
isNormal Ranges objects
isNormal-method IRanges and NormalIRanges objects
isNormal-method List of IRanges and NormalIRanges
isNormal-method Ranges objects
iteratorFun Applying over spaces
iteratorFun-method Applying over spaces
iteratorFun<- Applying over spaces
iteratorFun<--method Applying over spaces

-- L --

lapply-method Lists of Atomic Vectors in Natural and Rle Form
lapply-method List objects
lapply-method Data on ranges
lapply-method Simple and Compressed List Classes
length-method GappedRanges objects
length-method Grouping objects
length-method Set of hits between 2 vector-like objects
length-method Interval Search Forests
length-method Interval Search Trees
length-method MaskCollection objects
length-method Data on ranges
length-method Ranges objects
length-method Mapping of ranges to another sequence
length-method Rle objects
length-method Simple and Compressed List Classes
length-method Views objects
length<--method Grouping objects
levels-method Rle objects
levels.Rle Rle objects
levels<--method Rle objects
List List objects
List-class List objects
LogicalList Lists of Atomic Vectors in Natural and Rle Form
LogicalList-class Lists of Atomic Vectors in Natural and Rle Form
low2high Grouping objects
low2high-method Grouping objects

-- M --

mad-method Lists of Atomic Vectors in Natural and Rle Form
mad-method Rle objects
mad.Rle Rle objects
map Mapping of ranges to another sequence
Map-method Functional programming methods for List objects
Mask MaskCollection objects
MaskCollection MaskCollection objects
MaskCollection-class MaskCollection objects
MaskCollection.show_frame MaskCollection objects
maskedratio MaskCollection objects
maskedratio-method MaskCollection objects
maskedwidth MaskCollection objects
maskedwidth-method MaskCollection objects
match-method Set of hits between 2 vector-like objects
match-method Comparing and ordering ranges
match-method Rle objects
Math-method Lists of Atomic Vectors in Natural and Rle Form
Math-method Rle objects
Math2-method Lists of Atomic Vectors in Natural and Rle Form
Math2-method Rle objects
max-method IRanges and NormalIRanges objects
max-method List of IRanges and NormalIRanges
max-method MaskCollection objects
max-method Summarize views on a vector-like object with numeric values
mcols Vector objects
mcols-method Vector objects
mcols<- Vector objects
mcols<--method Vector objects
mean-method Lists of Atomic Vectors in Natural and Rle Form
mean-method Rle objects
mean-method Summarize views on a vector-like object with numeric values
mean.Rle Rle objects
median-method Lists of Atomic Vectors in Natural and Rle Form
median-method Rle objects
median.Rle Rle objects
members Grouping objects
members-method Grouping objects
mendoapply Endomorphisms via application of a function over an object's elements
mendoapply-method List objects
mendoapply-method Simple and Compressed List Classes
mendoapply-method Endomorphisms via application of a function over an object's elements
merge-method The DataTable API
merge-method List of Ranges
metadata Annotated class
metadata-method Annotated class
metadata<- Annotated class
metadata<--method Annotated class
mid Ranges objects
mid-method Ranges objects
min-method IRanges and NormalIRanges objects
min-method List of IRanges and NormalIRanges
min-method MaskCollection objects
min-method Summarize views on a vector-like object with numeric values
mseqapply Apply function and cast to Vector
mstack Vector objects
mstack-method External Data Frame
mstack-method Vector objects
multisplit Split elements belonging to multiple groups

-- N --

na.exclude The DataTable API
na.exclude-method The DataTable API
na.omit The DataTable API
na.omit-method The DataTable API
names-method GappedRanges objects
names-method Grouping objects
names-method IRanges and NormalIRanges objects
names-method Interval Search Forests
names-method MaskCollection objects
names-method Data on ranges
names-method Simple and Compressed List Classes
names-method Views objects
names<--method GappedRanges objects
names<--method Grouping objects
names<--method IRanges and NormalIRanges objects
names<--method MaskCollection objects
names<--method Data on ranges
names<--method Simple and Compressed List Classes
names<--method Views objects
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
nchar-method Rle objects
NCOL-method The DataTable API
ncol-method External Data Frame
ncol-method List of DataFrames
ncol-method Data on ranges
nearest Finding the nearest range neighbor
nearest-method Finding the nearest range neighbor
nearest-methods Finding the nearest range neighbor
newViews Views objects
ngap GappedRanges objects
ngap-method GappedRanges objects
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 The DataTable API
NROW-method Vector objects
nrow-method External Data Frame
nrow-method List of DataFrames
nrow-method Data on ranges
nrun Rle objects
nrun-method Rle objects
NumericList Lists of Atomic Vectors in Natural and Rle Form
NumericList-class Lists of Atomic Vectors in Natural and Rle Form

-- O --

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

-- P --

params Collection of Filter Rules
params-method Collection of Filter Rules
Partitioning Grouping objects
Partitioning-class Grouping objects
PartitioningByEnd Grouping objects
PartitioningByEnd-class Grouping objects
PartitioningByWidth Grouping objects
PartitioningByWidth-class Grouping objects
paste-method Rle objects
pgap Set operations on IRanges, RangesList, and Hits objects
pgap-method Set operations on IRanges, RangesList, and Hits objects
pintersect Set operations on IRanges, RangesList, and Hits objects
pintersect-method Set operations on IRanges, RangesList, and Hits objects
pmap Mapping of ranges to another sequence
pmax-method Lists of Atomic Vectors in Natural and Rle Form
pmax-method Rle objects
pmax.int-method Lists of Atomic Vectors in Natural and Rle Form
pmax.int-method Rle objects
pmin-method Lists of Atomic Vectors in Natural and Rle Form
pmin-method Rle objects
pmin.int-method Lists of Atomic Vectors in Natural and Rle Form
pmin.int-method Rle objects
Position-method Functional programming methods for List objects
precede Finding the nearest range neighbor
precede-method Finding the nearest range neighbor
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, RangesList, and Hits objects
psetdiff-method Set operations on IRanges, RangesList, and Hits objects
punion Set operations on IRanges, RangesList, and Hits objects
punion-method Set operations on IRanges, RangesList, and Hits objects

-- Q --

quantile-method Lists of Atomic Vectors in Natural and Rle Form
quantile-method Rle objects
quantile.Rle Rle objects
queryHits Set of hits between 2 vector-like objects
queryHits-method Set of hits between 2 vector-like objects
queryHits-method List of Hits objects
queryHits-method Mapping of ranges to another sequence
queryLength Set of hits between 2 vector-like objects
queryLength-method Set of hits between 2 vector-like objects
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 Data on ranges
ranges-method Selection of ranges and columns
ranges-method Mapping of ranges to another sequence
ranges-method Rle objects
ranges-method Views objects
ranges-method List of Views
ranges-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
RangesMapping-class Mapping of ranges to another sequence
RangesORmissing Finding the nearest range neighbor
RangesORmissing-class Finding the nearest range neighbor
rank-method Comparing and ordering ranges
RawList Lists of Atomic Vectors in Natural and Rle Form
RawList-class Lists of Atomic Vectors in Natural and Rle Form
rbind-method External Data Frame
rbind-method List of DataFrames
rbind-method The DataTable API
rbind-method Matrix for Filter Results
rbind-method Data on ranges
rdapply Applying over spaces
rdapply-method Applying over spaces
RDApplyParams Applying over spaces
RDApplyParams-class Applying over spaces
read.agpMask Read a mask from a file
read.gapMask Read a mask from a file
read.liftMask Read a mask from a file
read.Mask Read a mask from a file
read.rmMask Read a mask from a file
read.trfMask Read a mask from a file
reduce Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
Reduce-method Functional programming methods for List objects
reduce-method Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
reducerFun Applying over spaces
reducerFun-method Applying over spaces
reducerFun<- Applying over spaces
reducerFun<--method Applying over spaces
reducerParams Applying over spaces
reducerParams-method Applying over spaces
reducerParams<- Applying over spaces
reducerParams<--method Applying over spaces
reflect Intra range transformations of a Ranges, Views, RangesList, 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
remapHits Set of hits between 2 vector-like objects
rename Vector objects
rename-method Vector objects
rep-method Rle objects
rep-method Vector objects
rep.int-method Rle objects
rep.int-method Vector objects
resize Intra range transformations of a Ranges, Views, RangesList, 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 Rle objects
rev-method Vector objects
rev.Rle Rle objects
revElements List objects
revElements-method List objects
revElements-method Simple and Compressed List Classes
reverse reverse
reverse-method reverse
Rle Rle objects
Rle-class Rle objects
Rle-method Rle objects
RleList Lists of Atomic Vectors in Natural and Rle Form
RleList-class Lists of Atomic Vectors in Natural and Rle Form
RleList-method Lists of Atomic Vectors in Natural and Rle Form
RleViews The RleViews class
RleViews-class The RleViews class
RleViewsList List of RleViews
RleViewsList-class List of RleViews
rownames-method External Data Frame
rownames-method List of DataFrames
rownames-method Data on ranges
rownames<--method External Data Frame
rownames<--method List of DataFrames
rownames<--method Data on ranges
runLength Rle objects
runLength-method Lists of Atomic Vectors in Natural and Rle Form
runLength-method Rle objects
runLength<- Rle objects
runLength<--method Rle objects
runmean Fixed width running window summaries across vector-like objects
runmean-method Lists of Atomic Vectors in Natural and Rle Form
runmean-method Rle objects
runmed-method Lists of Atomic Vectors in Natural and Rle Form
runmed-method Rle objects
runq Fixed width running window summaries across vector-like objects
runq-method Lists of Atomic Vectors in Natural and Rle Form
runq-method Rle objects
runstat Fixed width running window summaries across vector-like objects
runsum Fixed width running window summaries across vector-like objects
runsum-method Lists of Atomic Vectors in Natural and Rle Form
runsum-method Rle objects
runValue Rle objects
runValue-method Lists of Atomic Vectors in Natural and Rle Form
runValue-method Rle objects
runValue<- Rle objects
runValue<--method Lists of Atomic Vectors in Natural and Rle Form
runValue<--method Rle objects
runwtsum Fixed width running window summaries across vector-like objects
runwtsum-method Lists of Atomic Vectors in Natural and Rle Form
runwtsum-method Rle objects

-- S --

safeExplode Some utility functions to operate on strings
sapply-method List objects
score Score accessor and setter
score-method Data on ranges
score<- Score accessor and setter
score<--method Data on ranges
sd-method Lists of Atomic Vectors in Natural and Rle Form
sd-method Rle objects
selfmatch Compare, order, tabulate vector-like objects
selfmatch-method Comparing and ordering ranges
selfmatch-method Compare, order, tabulate vector-like objects
seqapply Apply function and cast to Vector
seqby Apply function and cast to Vector
seqselect Vector objects
seqselect<- Vector objects
seqsplit Apply function and cast to Vector
setdiff-method Rle objects
setdiff-method Set operations on IRanges, RangesList, and Hits objects
setops-methods Set operations on IRanges, RangesList, and Hits 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
shiftApply-method Rle objects
shiftApply-method Vector objects
show-method Lists of Atomic Vectors in Natural and Rle Form
show-method List of DataFrames
show-method The DataTable API
show-method Matrix for Filter Results
show-method Collection of Filter Rules
show-method GappedRanges objects
show-method Grouping objects
show-method Set of hits between 2 vector-like objects
show-method Interval Search Forests
show-method List objects
show-method MaskCollection objects
show-method Data on ranges
show-method Ranges objects
show-method List of Ranges
show-method Rle objects
show-method The RleViews class
showAsCell Vector objects
showAsCell-method Lists of Atomic Vectors in Natural and Rle Form
showAsCell-method Ranges objects
showAsCell-method List of Ranges
showAsCell-method Rle objects
showAsCell-method Vector objects
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
SimpleIntegerList Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleIRangesList List of IRanges and NormalIRanges
SimpleIRangesList-class List of IRanges and NormalIRanges
SimpleList Simple and Compressed List Classes
SimpleList-class Simple and Compressed List Classes
SimpleLogicalList Lists of Atomic Vectors in Natural and Rle Form
SimpleLogicalList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleNormalIRangesList List of IRanges and NormalIRanges
SimpleNormalIRangesList-class List of IRanges and NormalIRanges
SimpleNumericList Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRangesList List of Ranges
SimpleRangesList-class List of Ranges
SimpleRawList Lists of Atomic Vectors in Natural and Rle Form
SimpleRawList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList-class Lists of Atomic Vectors in Natural and Rle Form
SimpleRleViewsList-class List of RleViews
SimpleSplitDataFrameList-class List of DataFrames
SimpleViewsList List of Views
SimpleViewsList-class List of Views
simplify Applying over spaces
simplify-method Applying over spaces
simplify<- Applying over spaces
simplify<--method Applying over spaces
slice 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
smoothEnds-method Rle objects
solveUserSEW The IRanges constructor and supporting functions
solveUserSEW0 The IRanges constructor and supporting functions
sort-method Rle objects
sort-method Compare, order, tabulate vector-like objects
sort.Rle Rle objects
sort.Vector Compare, order, tabulate vector-like objects
space List of Ranges
space-method List of Hits objects
space-method Data on ranges
space-method List of Ranges
space-method Mapping of ranges to another sequence
split-method Data on ranges
split-method Group elements of a vector-like object into a list-like object
split<--method Apply function and cast to Vector
splitAsList Group elements of a vector-like object into a list-like object
splitAsListReturnedClass Group elements of a vector-like object into a list-like object
splitAsListReturnedClass-method Group elements of a vector-like object into a list-like object
SplitDataFrameList List of DataFrames
SplitDataFrameList-class List of DataFrames
splitRanges Rle objects
splitRanges-method Rle objects
stack-method List of DataFrames
stack-method List objects
stack-method Lists of RangedData
start-method GappedRanges objects
start-method Grouping objects
start-method IRanges and NormalIRanges objects
start-method List of IRanges and NormalIRanges
start-method Interval Search Forests
start-method Interval Search Trees
start-method Data on ranges
start-method Ranges objects
start-method List of Ranges
start-method Rle objects
start-method Views objects
start-method List of Views
start<- Ranges objects
start<--method IRanges and NormalIRanges objects
start<--method Data on ranges
start<--method List of Ranges
start<--method Views objects
strsplitAsListOfIntegerVectors Some utility functions to operate on strings
sub-method Lists of Atomic Vectors in Natural and Rle Form
sub-method Rle objects
subject Views objects
subject-method List of RleViews
subject-method Views objects
subjectHits Set of hits between 2 vector-like objects
subjectHits-method Set of hits between 2 vector-like objects
subjectHits-method List of Hits objects
subjectHits-method Mapping of ranges to another sequence
subjectLength Set of hits between 2 vector-like objects
subjectLength-method Set of hits between 2 vector-like objects
subjectLength-method List of Hits objects
subset-method The DataTable API
subset-method Vector objects
subsetByFilter Collection of Filter Rules
subsetByFilter-method Collection of Filter Rules
subsetByOverlaps Finding overlapping ranges
subsetByOverlaps-method Finding overlapping ranges
subsetByRanges Vector objects
substr-method Rle objects
substring-method Rle objects
subviews Views objects
subviews-method Views objects
successiveIRanges IRanges utility functions
successiveViews Views objects
sum-method Lists of Atomic Vectors in Natural and Rle Form
sum-method Summarize views on a vector-like object with numeric values
Summary-method Lists of Atomic Vectors in Natural and Rle Form
Summary-method Rle objects
Summary-method Summarize views on a vector-like object with numeric values
summary-method Matrix for Filter Results
summary-method Collection of Filter Rules
summary-method List of IRanges and NormalIRanges
summary-method Rle objects
summary.Rle Rle objects
svn.time Some utility functions to operate on strings

-- T --

t-method Set of hits between 2 vector-like objects
t-method List of Hits objects
table-method Lists of Atomic Vectors in Natural and Rle Form
table-method Rle objects
table-method Compare, order, tabulate vector-like objects
tail-method Vector objects
tail.Vector Vector objects
tapply-method Vector objects
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
tofactor Grouping objects
togroup Grouping objects
togroup-method Grouping objects
togrouplength Grouping objects
togrouplength-method Grouping objects
togrouprank Grouping objects
togrouprank-method Grouping objects
tolower-method Lists of Atomic Vectors in Natural and Rle Form
tolower-method Rle objects
toupper-method Lists of Atomic Vectors in Natural and Rle Form
toupper-method Rle objects
trim Views objects
trim-method Views objects
tseqapply Apply function and cast to Vector

-- U --

union-method Rle objects
union-method Set operations on IRanges, RangesList, and Hits objects
unique-method Lists of Atomic Vectors in Natural and Rle Form
unique-method The DataTable API
unique-method Rle objects
unique-method Compare, order, tabulate vector-like objects
unique.CompressedRleList Lists of Atomic Vectors in Natural and Rle Form
unique.DataTable The DataTable API
unique.Rle Rle objects
unique.SimpleRleList Lists of Atomic Vectors in Natural and Rle Form
unique.Vector Compare, order, tabulate vector-like objects
universe List of Ranges
universe-method Data on ranges
universe-method List of Ranges
universe-method List of Views
universe<- List of Ranges
universe<--method Data on ranges
universe<--method List of Ranges
universe<--method List of Views
unlist-method List of IRanges and NormalIRanges
unlist-method List objects
unlist-method Lists of RangedData
unlist-method Ranges objects
unlist-method Simple and Compressed List Classes
unsplit-method Apply function and cast to Vector
unstrsplit Some utility functions to operate on strings
unstrsplit-method Lists of Atomic Vectors in Natural and Rle Form
unstrsplit-method Some utility functions to operate on strings
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 Vector objects
values-method Data on ranges
values-method Vector objects
values<- Vector objects
values<--method Data on ranges
values<--method Vector objects
var-method Lists of Atomic Vectors in Natural and Rle Form
var-method Rle objects
Vector Vector objects
Vector-class Vector objects
Vector-comparison Compare, order, tabulate vector-like 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 Lists of Atomic Vectors in Natural and Rle Form
which-method Rle objects
which.max-method Lists of Atomic Vectors in Natural and Rle Form
which.max-method Rle objects
which.max-method 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 List of IRanges and NormalIRanges
whichFirstNotNormal-method Ranges objects
width Ranges objects
width-method Grouping objects
width-method IRanges and NormalIRanges objects
width-method List of IRanges and NormalIRanges
width-method Interval Search Forests
width-method MaskCollection objects
width-method Data on ranges
width-method Ranges objects
width-method List of Ranges
width-method Rle objects
width-method Views objects
width-method List of Views
width<- Ranges objects
width<--method IRanges and NormalIRanges objects
width<--method Data on ranges
width<--method List of Ranges
width<--method Views objects
window-method Rle objects
window-method Vector objects
window.factor Vector objects
window.NULL Vector objects
window.Rle Rle objects
window.Vector Vector objects
window.vector Vector objects
window<--method The DataTable API
window<--method Vector objects
window<-.DataTable The DataTable API
window<-.factor Vector objects
window<-.Vector Vector objects
window<-.vector Vector objects
with-method List objects
with-method Vector objects
within-method List objects
within-method Data on ranges

-- X --

xtabs-method Statistical modeling with DataTable

-- misc --

!-method Rle objects
!=-method Compare, order, tabulate vector-like objects
$-method List objects
$<--method List objects
$<--method Data on ranges
$<--method Simple and Compressed List Classes
%in%-method Rle objects
%in%-method Compare, order, tabulate vector-like objects
%outside% Finding overlapping ranges
%over% Finding overlapping ranges
%within% Finding overlapping ranges
<-method Compare, order, tabulate vector-like objects
<=-method Compare, order, tabulate vector-like objects
==-method Compare, order, tabulate vector-like objects
>-method Compare, order, tabulate vector-like objects
>=-method Compare, order, tabulate vector-like objects
[-method External Data Frame
[-method List of DataFrames
[-method Matrix for Filter Results
[-method Collection of Filter Rules
[-method Interval Search Forests
[-method List objects
[-method MaskCollection objects
[-method Data on ranges
[-method Rle objects
[-method Simple and Compressed List Classes
[-method Vector objects
[<--method External Data Frame
[<--method List of DataFrames
[<--method List objects
[<--method Rle objects
[<--method Vector objects
[[-method List objects
[[-method Data on ranges
[[<--method External Data Frame
[[<--method Collection of Filter Rules
[[<--method List objects
[[<--method Data on ranges
[[<--method Simple and Compressed List Classes