Foundation of integer range manipulation in Bioconductor

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Documentation for package ‘IRanges’ version 2.43.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D E F G H I L M N O P Q R S T U V W misc

-- A --

active	MaskCollection objects
active-method	MaskCollection objects
active<-	MaskCollection objects
active<--method	MaskCollection objects
all-method	Common operations on AtomicList objects
any-method	Common operations on AtomicList objects
anyNA-method	Common operations on AtomicList objects
append-method	MaskCollection objects
as.character-method	IPosRanges objects
as.data.frame-method	IPos objects
as.data.frame-method	IPosRanges objects
as.data.frame.IPos	IPos objects
as.data.frame.IPosRanges	IPosRanges objects
as.env-method	List of DataFrames
as.factor-method	IPosRanges objects
as.list-method	Lists of Atomic Vectors in Natural and Rle Form
as.list-method	Examples of basic manipulation of Hits objects
as.list-method	List of IRanges and NormalIRanges
as.matrix-method	Lists of Atomic Vectors in Natural and Rle Form
as.matrix-method	CompressedHitsList objects
as.matrix-method	IPosRanges objects
as.matrix-method	Views objects
as.matrix-method	List of Views
as.vector-method	Lists of Atomic Vectors in Natural and Rle Form
asNormalIRanges	IRanges utility functions
AtomicList	Lists of Atomic Vectors in Natural and Rle Form
AtomicList-class	Lists of Atomic Vectors in Natural and Rle Form
AtomicList-utils	Common operations on AtomicList objects

-- B --

bindROWS-method	CompressedList objects
bindROWS-method	Grouping objects
bindROWS-method	IPos objects
bindROWS-method	Nested Containment List objects
bindROWS-method	Views objects
breakInChunks	IRanges utility functions

-- C --

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:CompressedDataFrameList	List of DataFrames
class:CompressedDFrameList	List of DataFrames
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:CompressedSplitDataFrameList	List of DataFrames
class:CompressedSplitDFrameList	List of DataFrames
class:DataFrameList	List of DataFrames
class:DFrameList	List of DataFrames
class:Dups	Grouping objects
class:FactorList	Lists of Atomic Vectors in Natural and Rle Form
class:Grouping	Grouping objects
class:GroupingIRanges	Grouping objects
class:GroupingRanges	Grouping objects
class:H2LGrouping	Grouping objects
class:IntegerList	Lists of Atomic Vectors in Natural and Rle Form
class:IntegerRanges	IntegerRanges objects
class:IntegerRangesList	IntegerRangesList objects
class:IntegerRanges_OR_missing	Finding the nearest range/position neighbor
class:IPos	IPos objects
class:IPosRanges	IPosRanges objects
class:IRanges	IRanges and NormalIRanges objects
class:IRangesList	List of IRanges and NormalIRanges
class:LogicalList	Lists of Atomic Vectors in Natural and Rle Form
class:ManyToManyGrouping	Grouping objects
class:ManyToOneGrouping	Grouping objects
class:MaskCollection	MaskCollection objects
class:NCList	Nested Containment List objects
class:NCLists	Nested Containment List objects
class:NormalIRanges	IRanges and NormalIRanges objects
class:NormalIRangesList	List of IRanges and NormalIRanges
class:NumericList	Lists of Atomic Vectors in Natural and Rle Form
class:Partitioning	Grouping objects
class:PartitioningByEnd	Grouping objects
class:PartitioningByWidth	Grouping objects
class:PartitioningMap	Grouping objects
class: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:SimpleDataFrameList	List of DataFrames
class:SimpleDFrameList	List of DataFrames
class:SimpleFactorList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleGrouping	Grouping objects
class:SimpleIntegerList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleIntegerRangesList	IntegerRangesList objects
class:SimpleIRangesList	List of IRanges and NormalIRanges
class:SimpleLogicalList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleManyToManyGrouping	Grouping objects
class:SimpleManyToOneGrouping	Grouping objects
class:SimpleNormalIRangesList	List of IRanges and NormalIRanges
class:SimpleNumericList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleRawList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleRleList	Lists of Atomic Vectors in Natural and Rle Form
class:SimpleSplitDataFrameList	List of DataFrames
class:SimpleSplitDFrameList	List of DataFrames
class:SimpleViewsList	List of Views
class:SplitDataFrameList	List of DataFrames
class:SplitDFrameList	List of DataFrames
class:StitchedIPos	IPos objects
class:UnstitchedIPos	IPos objects
class:Views	Views objects
class:ViewsList	List of Views
classNameForDisplay-method	CompressedList objects
classNameForDisplay-method	List of DataFrames
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	IPos objects
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	Selection of ranges and columns
coerce-method	Rle objects (old man page)
coerce-method	List of RleViews
coerce-method	Views objects
collapse	MaskCollection objects
collapse-method	MaskCollection objects
colnames-method	List of DataFrames
colnames-method	Selection of ranges and columns
colnames<--method	List of DataFrames
colnames<--method	Selection of ranges and columns
columnMetadata	List of DataFrames
columnMetadata-method	List of DataFrames
columnMetadata<-	List of DataFrames
columnMetadata<--method	List of DataFrames
commonColnames	List of DataFrames
commonColnames-method	List of DataFrames
commonColnames<-	List of DataFrames
commonColnames<--method	List of DataFrames
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
CompressedDataFrameList	List of DataFrames
CompressedDataFrameList-class	List of DataFrames
CompressedDFrameList	List of DataFrames
CompressedDFrameList-class	List of DataFrames
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	List of DataFrames
CompressedSplitDataFrameList-class	List of DataFrames
CompressedSplitDFrameList	List of DataFrames
CompressedSplitDFrameList-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 --

DataFrameList	List of DataFrames
DataFrameList-class	List of DataFrames
desc	MaskCollection objects
desc-method	MaskCollection objects
desc<-	MaskCollection objects
desc<--method	MaskCollection objects
DFrameList	List of DataFrames
DFrameList-class	List of DataFrames
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
dims-method	List of DataFrames
disjoin	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjoin-method	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjointBins	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
disjointBins-method	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
distance	Finding the nearest range/position neighbor
distance-method	Finding the nearest range/position neighbor
distanceToNearest	Finding the nearest range/position neighbor
distanceToNearest-method	Finding the nearest range/position neighbor
drop-method	Lists of Atomic Vectors in Natural and Rle Form
duplicated-method	Lists of Atomic Vectors in Natural and Rle Form
duplicated-method	Grouping objects
Dups	Grouping objects
Dups-class	Grouping objects

-- E --

elementNROWS-method	CompressedList objects
elementNROWS-method	IPosRanges objects
elementNROWS-method	Nested Containment List objects
end-method	Grouping objects
end-method	IPosRanges objects
end-method	List of IRanges and NormalIRanges
end-method	IntegerRangesList objects
end-method	Nested Containment List objects
end-method	List of Views
end<-	IPosRanges objects
end<--method	IRanges and NormalIRanges objects
end<--method	IntegerRangesList objects
end<--method	Views objects
endsWith-method	Common operations on AtomicList objects
equisplit	Extract list fragments from a list-like object
eval	Vector objects (old man page)
eval-method	Vector objects (old man page)
extractList	Group elements of a vector-like object into a list-like object
extractList-method	Group elements of a vector-like object into a list-like object
extractListFragments	Extract list fragments from a list-like object
extractROWS-method	Grouping objects
extractROWS-method	IPos objects
extractROWS-method	Nested Containment List objects

-- F --

FactorList	Lists of Atomic Vectors in Natural and Rle Form
FactorList-class	Lists of Atomic Vectors in Natural and Rle Form
findOverlapPairs	Finding overlapping ranges
findOverlaps	Finding overlapping ranges
findOverlaps-method	Finding overlapping ranges
findOverlaps-methods	Finding overlapping ranges
findRange	Rle objects (old man page)
findRange-method	Rle objects (old man page)
flank	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
flank-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
follow	Finding the nearest range/position neighbor
follow-method	Finding the nearest range/position neighbor
from-method	CompressedHitsList objects

-- G --

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

-- H --

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

-- I --

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

-- L --

lapply-method	Lists of Atomic Vectors in Natural and Rle Form
lapply-method	CompressedList objects
length-method	CompressedList objects
length-method	Grouping objects
length-method	IPos objects
length-method	IPosRanges objects
length-method	MaskCollection objects
length-method	Nested Containment List 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
merge-method	IntegerRangesList objects
mergeByOverlaps	Finding overlapping ranges
mid	IPosRanges objects
mid-method	IPosRanges objects
min-method	IRanges and NormalIRanges objects
min-method	List of IRanges and NormalIRanges
min-method	MaskCollection objects
min-method	Summarize views on a vector-like object with numeric values
multisplit	Split elements belonging to multiple groups

-- N --

names-method	CompressedList objects
names-method	Grouping objects
names-method	IPos objects
names-method	IRanges and NormalIRanges objects
names-method	MaskCollection objects
names-method	Nested Containment List objects
names-method	Views objects
names<--method	CompressedList objects
names<--method	Grouping objects
names<--method	IPos objects
names<--method	IRanges and NormalIRanges objects
names<--method	MaskCollection objects
names<--method	Views objects
narrow	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
narrow-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
nchar-method	Common operations on AtomicList objects
NCList	Nested Containment List objects
NCList-class	Nested Containment List objects
NCLists	Nested Containment List objects
NCLists-class	Nested Containment List objects
ncol-method	List of DataFrames
ncols-method	List of DataFrames
nearest	Finding the nearest range/position neighbor
nearest-method	Finding the nearest range/position neighbor
nearest-methods	Finding the nearest range/position 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	List of DataFrames
nrows-method	List of DataFrames
NumericList	Lists of Atomic Vectors in Natural and Rle Form
NumericList-class	Lists of Atomic Vectors in Natural and Rle Form

-- O --

Ops-method	Common operations on AtomicList objects
Ops-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
order-method	Lists of Atomic Vectors in Natural and Rle Form
order-method	Common operations on AtomicList objects
order-method	Comparing and ordering ranges
overlapsAny	Finding overlapping ranges
overlapsAny-method	Finding overlapping ranges
overlapsRanges	Finding overlapping ranges
overlapsRanges-method	Finding overlapping ranges

-- P --

parallel_slot_names-method	Grouping objects
parallel_slot_names-method	IPos objects
parallel_slot_names-method	IRanges and NormalIRanges objects
parallel_slot_names-method	Nested Containment List objects
parallel_slot_names-method	Views objects
Partitioning	Grouping objects
Partitioning-class	Grouping objects
PartitioningByEnd	Grouping objects
PartitioningByEnd-class	Grouping objects
PartitioningByWidth	Grouping objects
PartitioningByWidth-class	Grouping objects
PartitioningMap	Grouping objects
PartitioningMap-class	Grouping objects
paste-method	Common operations on AtomicList objects
pcompare	Comparing and ordering ranges
pcompare-method	Comparing and ordering ranges
pgap	Set operations on IntegerRanges and IntegerRangesList objects
pgap-method	Set operations on IntegerRanges and IntegerRangesList objects
pintersect	Set operations on IntegerRanges and IntegerRangesList objects
pintersect-method	Set operations on IntegerRanges and IntegerRangesList objects
pmax-method	Common operations on AtomicList objects
pmax.int-method	Common operations on AtomicList objects
pmin-method	Common operations on AtomicList objects
pmin.int-method	Common operations on AtomicList objects
pos	IPos objects
pos-method	IPos objects
pos-method	List of IRanges and NormalIRanges
pos-method	IntegerRangesList objects
poverlaps	Finding overlapping ranges
poverlaps-method	Finding overlapping ranges
precede	Finding the nearest range/position neighbor
precede-method	Finding the nearest range/position neighbor
promoters	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
promoters-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
psetdiff	Set operations on IntegerRanges and IntegerRangesList objects
psetdiff-method	Set operations on IntegerRanges and IntegerRangesList objects
punion	Set operations on IntegerRanges and IntegerRangesList objects
punion-method	Set operations on IntegerRanges and IntegerRangesList objects

-- Q --

quantile-method

Common operations on AtomicList objects

-- R --

range	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
range-method	Common operations on AtomicList objects
range-method	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
range-squeezers	Squeeze the ranges out of a range-based object
rangeComparisonCodeToLetter	Comparing and ordering ranges
RangedSelection	Selection of ranges and columns
RangedSelection-class	Selection of ranges and columns
ranges	Squeeze the ranges out of a range-based object
ranges-method	Lists of Atomic Vectors in Natural and Rle Form
ranges-method	IRanges and NormalIRanges objects
ranges-method	Nested Containment List objects
ranges-method	Selection of ranges and columns
ranges-method	Rle objects (old man page)
ranges-method	Views objects
ranges-method	List of Views
ranges<-	Views objects
ranges<--method	Selection of ranges and columns
ranges<--method	Views objects
rank-method	Lists of Atomic Vectors in Natural and Rle Form
rank-method	Common operations on AtomicList objects
RawList	Lists of Atomic Vectors in Natural and Rle Form
RawList-class	Lists of Atomic Vectors in Natural and Rle Form
rbind-method	List of DataFrames
read.agpMask	Read a mask from a file
read.gapMask	Read a mask from a file
read.liftMask	Read a mask from a file
read.Mask	Read a mask from a file
read.rmMask	Read a mask from a file
read.trfMask	Read a mask from a file
reduce	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
reduce-method	Inter range transformations of an IntegerRanges, Views, IntegerRangesList, or MaskCollection object
reflect	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
reflect-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
regroup	Group elements of a vector-like object into a list-like object
relist	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
resize	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
resize-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
restrict	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
restrict-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
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	List of DataFrames
ROWNAMES<--method	List of DataFrames
rownames<--method	List of DataFrames
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 --

sd-method	Common operations on AtomicList objects
selectNearest	Finding the nearest range/position neighbor
selfmatch-method	Common operations on AtomicList objects
selfmatch-method	Comparing and ordering ranges
setdiff	Set operations on IntegerRanges and IntegerRangesList objects
setdiff-method	Set operations on IntegerRanges and IntegerRangesList objects
setops-methods	Set operations on IntegerRanges and IntegerRangesList objects
shift	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
shift-method	Intra range transformations of an IRanges, IPos, Views, RangesList, or MaskCollection object
show-method	Lists of Atomic Vectors in Natural and Rle Form
show-method	List of DataFrames
show-method	Grouping objects
show-method	IPos objects
show-method	IPosRanges objects
show-method	IntegerRangesList objects
show-method	MaskCollection objects
show-method	The RleViews class
SimpleAtomicList	Lists of Atomic Vectors in Natural and Rle Form
SimpleAtomicList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList	Lists of Atomic Vectors in Natural and Rle Form
SimpleCharacterList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList	Lists of Atomic Vectors in Natural and Rle Form
SimpleComplexList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleDataFrameList	List of DataFrames
SimpleDataFrameList-class	List of DataFrames
SimpleDFrameList	List of DataFrames
SimpleDFrameList-class	List of DataFrames
SimpleFactorList	Lists of Atomic Vectors in Natural and Rle Form
SimpleFactorList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleGrouping-class	Grouping objects
SimpleIntegerList	Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleIntegerRangesList	IntegerRangesList objects
SimpleIntegerRangesList-class	IntegerRangesList objects
SimpleIRangesList	List of IRanges and NormalIRanges
SimpleIRangesList-class	List of IRanges and NormalIRanges
SimpleLogicalList	Lists of Atomic Vectors in Natural and Rle Form
SimpleLogicalList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleManyToManyGrouping-class	Grouping objects
SimpleManyToOneGrouping-class	Grouping objects
SimpleNormalIRangesList	List of IRanges and NormalIRanges
SimpleNormalIRangesList-class	List of IRanges and NormalIRanges
SimpleNumericList	Lists of Atomic Vectors in Natural and Rle Form
SimpleNumericList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRawList	Lists of Atomic Vectors in Natural and Rle Form
SimpleRawList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleList-class	Lists of Atomic Vectors in Natural and Rle Form
SimpleRleViewsList-class	List of RleViews
SimpleSplitDataFrameList	List of DataFrames
SimpleSplitDataFrameList-class	List of DataFrames
SimpleSplitDFrameList	List of DataFrames
SimpleSplitDFrameList-class	List of DataFrames
SimpleViewsList	List of Views
SimpleViewsList-class	List of Views
slice	Slice a vector-like or list-like object
slice-method	Slice a vector-like or list-like object
slice-methods	Slice a vector-like or list-like object
slidingWindows	IPosRanges objects
slidingWindows-method	IPosRanges objects
smoothEnds-method	Common operations on AtomicList objects
solveUserSEW	The IRanges constructor and supporting functions
sort-method	Lists of Atomic Vectors in Natural and Rle Form
space	IntegerRangesList objects
space-method	CompressedHitsList objects
space-method	IntegerRangesList objects
split<--method	2 methods that should be documented somewhere else
SplitDataFrameList	List of DataFrames
SplitDataFrameList-class	List of DataFrames
SplitDFrameList	List of DataFrames
SplitDFrameList-class	List of DataFrames
splitRanges	Rle objects (old man page)
splitRanges-method	Rle objects (old man page)
stack-method	List of DataFrames
start-method	Grouping objects
start-method	IPosRanges objects
start-method	IRanges and NormalIRanges objects
start-method	List of IRanges and NormalIRanges
start-method	IntegerRangesList objects
start-method	Nested Containment List objects
start-method	Views objects
start-method	List of Views
start<-	IPosRanges objects
start<--method	IRanges and NormalIRanges objects
start<--method	IntegerRangesList objects
start<--method	Views objects
startsWith-method	Common operations on AtomicList objects
StitchedIPos	IPos objects
StitchedIPos-class	IPos objects
sub-method	Common operations on AtomicList objects
subject	Views objects
subject-method	List of RleViews
subject-method	Views objects
subsetByOverlaps	Finding overlapping ranges
subsetByOverlaps-method	Finding overlapping ranges
subviews	Views objects
subviews-method	Views objects
successiveIRanges	IRanges utility functions
successiveViews	Views objects
sum-method	Common operations on AtomicList objects
sum-method	Summarize views on a vector-like object with numeric values
Summary-method	Common operations on AtomicList objects
Summary-method	Summarize views on a vector-like object with numeric values
summary-method	IPos objects
summary-method	IPosRanges objects
summary-method	List of IRanges and NormalIRanges
summary.IPos	IPos objects
summary.IPosRanges	IPosRanges objects

-- T --

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

-- U --

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

-- V --

var-method	Common operations on AtomicList objects
view-summarization-methods	Summarize views on a vector-like object with numeric values
viewApply	Summarize views on a vector-like object with numeric values
viewApply-method	Summarize views on a vector-like object with numeric values
viewMaxs	Summarize views on a vector-like object with numeric values
viewMaxs-method	Summarize views on a vector-like object with numeric values
viewMeans	Summarize views on a vector-like object with numeric values
viewMeans-method	Summarize views on a vector-like object with numeric values
viewMins	Summarize views on a vector-like object with numeric values
viewMins-method	Summarize views on a vector-like object with numeric values
viewRangeMaxs	Summarize views on a vector-like object with numeric values
viewRangeMaxs-method	Summarize views on a vector-like object with numeric values
viewRangeMins	Summarize views on a vector-like object with numeric values
viewRangeMins-method	Summarize views on a vector-like object with numeric values
Views	Views objects
Views-class	Views objects
Views-method	The RleViews class
Views-method	List of RleViews
ViewsList	List of Views
ViewsList-class	List of Views
viewSums	Summarize views on a vector-like object with numeric values
viewSums-method	Summarize views on a vector-like object with numeric values
viewWhichMaxs	Summarize views on a vector-like object with numeric values
viewWhichMaxs-method	Summarize views on a vector-like object with numeric values
viewWhichMins	Summarize views on a vector-like object with numeric values
viewWhichMins-method	Summarize views on a vector-like object with numeric values
vmembers	Grouping objects
vmembers-method	Grouping objects

-- W --

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

-- misc --

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