Foundation of integer range manipulation in Bioconductor


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Documentation for package ‘IRanges’ version 2.28.0

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

-- A --

active MaskCollection objects
active-method MaskCollection objects
active<- MaskCollection objects
active<--method MaskCollection objects
all-method Common operations on AtomicList objects
any-method Common operations on AtomicList objects
anyNA-method Common operations on AtomicList objects
append-method MaskCollection objects
as.character-method 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)
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