Infrastructure for manipulating intervals on sequences


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Documentation for package ‘IRanges’ version 1.6.16

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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

-- --

!-method Lists of Atomic Vectors in Natural and Rle Form
!-method Rle objects
!= Ranges comparison
!=-method Ranges comparison
!=-method Sequence objects
!=-method The XIntegerViews class
$-method Sequence objects
$<--method Data on ranges
$<--method Simple and Compressed List Classes
%in%-method Lists of Atomic Vectors in Natural and Rle Form
%in%-method Interval Search Trees
%in%-method Rle objects
< Ranges comparison
<-method Ranges comparison
<= Ranges comparison
<=-method Ranges comparison
== Ranges comparison
==-method Ranges comparison
==-method The XIntegerViews class
==-method XVector objects
> Ranges comparison
>-method Ranges comparison
>= Ranges comparison
>=-method Ranges comparison

-- 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 DataTable objects
aggregate-method Rle objects
aggregate-method Sequence objects
aggregate-method Simple and Compressed List Classes
Annotated Annotated class
Annotated-class Annotated class
append-method Collection of Filter Rules
append-method MaskCollection objects
append-method Sequence 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 Lists of Atomic Vectors in Natural and Rle Form
as.character-method Rle objects
as.complex-method Lists of Atomic Vectors in Natural and Rle Form
as.complex-method Rle objects
as.data.frame-method Lists of Atomic Vectors in Natural and Rle Form
as.data.frame-method External Data Frame
as.data.frame-method List of DataFrames
as.data.frame-method GappedRanges 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 XVectorList objects
as.env Sequence objects
as.env-method DataTable objects
as.env-method Data on ranges
as.env-method Sequence objects
as.factor-method Lists of Atomic Vectors in Natural and Rle Form
as.factor-method Rle objects
as.integer-method Lists of Atomic Vectors in Natural and Rle Form
as.integer-method Ranges objects
as.integer-method Rle objects
as.integer-method XVector objects
as.list-method Lists of Atomic Vectors in Natural and Rle Form
as.list-method List of IRanges and NormalIRanges
as.list-method Sequence objects
as.list-method Simple and Compressed List Classes
as.logical-method Lists of Atomic Vectors in Natural and Rle Form
as.logical-method Rle objects
as.matrix-method Ranges objects
as.matrix-method Matchings between Ranges
as.matrix-method List of Matchings between Ranges
as.numeric-method Lists of Atomic Vectors in Natural and Rle Form
as.numeric-method Rle objects
as.numeric-method XVector objects
as.raw-method Lists of Atomic Vectors in Natural and Rle Form
as.raw-method Rle objects
as.raw-method XVector objects
as.table-method Matchings between Ranges
as.table-method List of Matchings between Ranges
as.vector-method Lists of Atomic Vectors in Natural and Rle Form
as.vector-method Rle objects
as.vector-method XVector objects
asNormalIRanges IRanges utility functions
AtomicList-class Lists of Atomic Vectors in Natural and Rle Form

-- B --

Binning Grouping objects
Binning-class Grouping objects
by-method DataTable objects

-- 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 Sequence objects
c-method Simple and Compressed List Classes
c-method XVector objects
c-method XVectorList objects
cbind DataTable objects
cbind-method External Data Frame
cbind-method List of DataFrames
cbind-method DataTable objects
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:Binning Grouping objects
class:CompressedIRangesList List of IRanges and NormalIRanges
class:CompressedNormalIRangesList List of IRanges and NormalIRanges
class:DataTable DataTable objects
class:Dups Grouping objects
class:GappedRanges GappedRanges objects
class:GroupedIRanges XVectorList objects
class:Grouping Grouping objects
class:H2LGrouping Grouping objects
class:IRanges IRanges and NormalIRanges objects
class:IRangesList List of IRanges and NormalIRanges
class:MaskCollection MaskCollection objects
class:NormalIRanges IRanges and NormalIRanges objects
class:NormalIRangesList List of IRanges and NormalIRanges
class:Partitioning Grouping objects
class:PartitioningByEnd Grouping objects
class:PartitioningByWidth Grouping objects
class:Ranges Ranges objects
class:RangesList-class List of Ranges
class:Rle Rle objects
class:RleViews The RleViews class
class:Sequence Sequence objects
class:SimpleIRangesList List of IRanges and NormalIRanges
class:SimpleNormalIRangesList List of IRanges and NormalIRanges
class:SimpleRangesList-class List of Ranges
class:Views Views objects
class:XDouble XVector objects
class:XInteger XVector objects
class:XIntegerViews The XIntegerViews class
class:XRaw XVector objects
class:XRawList XVectorList objects
class:XVector XVector objects
class:XVectorList XVectorList objects
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 IRanges and NormalIRanges objects
coerce-method IRanges utility functions
coerce-method List of IRanges and NormalIRanges
coerce-method Interval Search Trees
coerce-method MaskCollection objects
coerce-method Data on ranges
coerce-method Selection of ranges and columns
coerce-method List of Ranges
coerce-method Rle objects
coerce-method List of RleViews
coerce-method Sequence objects
coerce-method Views objects
coerce-method XVector 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
complete.cases-method DataTable objects
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-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
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
countOverlap Interval Search Trees
countOverlaps Interval Search Trees
countOverlaps-method Interval Search Trees
cov-method Lists of Atomic Vectors in Natural and Rle Form
cov-method Rle objects
coverage Coverage across a set of ranges
coverage-method Coverage across a set of ranges
coverage.normargWidth Coverage across a set of ranges

-- D --

DataFrame External Data Frame
DataFrame-class External Data Frame
DataFrameList List of DataFrames
DataFrameList-class List of DataFrames
DataTable DataTable objects
DataTable-class DataTable objects
DataTable-stats Statistical modeling with DataTable
DataTableORNULL-class DataTable objects
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
dim-method List of DataFrames
dim-method DataTable objects
dim-method Matchings between Ranges
dimnames-method List of DataFrames
dimnames-method DataTable objects
dimnames<--method List of DataFrames
dimnames<--method DataTable objects
disjoin Making Ranges disjoint
disjoin-method RangesList utility functions
disjoin-method Making Ranges disjoint
disjointBins Making Ranges disjoint
disjointBins-method Making Ranges disjoint
duplicated-method Grouping objects
duplicated-method Ranges comparison
Dups Grouping objects
Dups-class Grouping objects

-- E --

elementLengths Sequence objects
elementLengths-method GappedRanges objects
elementLengths-method Data on ranges
elementLengths-method Ranges objects
elementLengths-method Sequence objects
elementMetadata Sequence objects
elementMetadata-method Sequence objects
elementMetadata<- Sequence objects
elementMetadata<--method Sequence objects
elementType Sequence objects
elementType-method Sequence objects
end-method GappedRanges objects
end-method Grouping objects
end-method List of IRanges and NormalIRanges
end-method Interval Search Trees
end-method Data on ranges
end-method Ranges objects
end-method List of Ranges
end-method Rle objects
end<- Ranges objects
end<--method IRanges and NormalIRanges objects
end<--method Data on ranges
end<--method List of Ranges
endoapply Endomorphisms via application of a function over an object's elements
endoapply-method Data on ranges
endoapply-method Sequence objects
endoapply-method Simple and Compressed List Classes
endoapply-method Endomorphisms via application of a function over an object's elements
eval-method Collection of Filter Rules
eval-method Sequence objects

-- F --

Filter-method Sequence objects
FilterRules Collection of Filter Rules
filterRules Applying over spaces
FilterRules-class Collection of Filter Rules
filterRules-method Applying over spaces
filterRules<- Applying over spaces
filterRules<--method Applying over spaces
Find-method Sequence objects
findOverlaps Interval Search Trees
findOverlaps-method Interval Search Trees
findRange Rle objects
findRange-method Rle objects
findRun Rle objects
findRun-method Rle objects
first Ranges objects
first-method Ranges objects
flank Ranges utility functions
flank-method Ranges utility functions
flank-method RangesList utility functions
follow Nearest neighbor finding
follow-method Nearest neighbor finding

-- G --

GappedRanges GappedRanges objects
GappedRanges-class GappedRanges objects
gaps Set operations on IRanges objects
gaps-method Set operations on IRanges objects
gaps-method MaskCollection objects
gaps-method RangesList utility functions
gaps-method Views objects
GroupedIRanges XVectorList objects
GroupedIRanges-class XVectorList objects
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 DataTable objects
head-method Sequence objects
high2low Grouping objects
high2low-method Grouping objects

-- I --

IntegerList Lists of Atomic Vectors in Natural and Rle Form
IntegerList-class Lists of Atomic Vectors in Natural and Rle Form
intersect-method Set operations on IRanges objects
intersect-method RangesList utility functions
IntervalTree Interval Search Trees
IntervalTree-class Interval Search Trees
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-setops Set operations on IRanges objects
IRanges-utils IRanges utility functions
IRangesList List of IRanges and NormalIRanges
IRangesList-class List of IRanges and NormalIRanges
is.na-method Lists of Atomic Vectors in Natural and Rle Form
is.na-method DataTable objects
is.na-method Rle objects
is.unsorted-method Rle objects
isDisjoint Ranges objects
isDisjoint-method List of IRanges and NormalIRanges
isDisjoint-method Ranges objects
isEmpty Sequence objects
isEmpty-method IRanges and NormalIRanges objects
isEmpty-method Ranges objects
isEmpty-method Sequence 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

-- L --

lapply-method Lists of Atomic Vectors in Natural and Rle Form
lapply-method Data on ranges
lapply-method Sequence objects
lapply-method Simple and Compressed List Classes
last Ranges objects
last-method Ranges objects
length-method GappedRanges objects
length-method Grouping objects
length-method Interval Search Trees
length-method MaskCollection objects
length-method Data on ranges
length-method Ranges objects
length-method Matchings between Ranges
length-method Rle objects
length-method Simple and Compressed List Classes
length-method XVector objects
length-method XVectorList objects
length<--method Grouping objects
levels-method Rle objects
levels<--method Rle 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
Map Sequence objects
Map-method Sequence objects
mapply Sequence objects
mapply-method Sequence 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 Lists of Atomic Vectors in Natural and Rle Form
match-method Interval Search Trees
match-method Rle objects
matchMatrix Matchings between Ranges
matchMatrix-method Matchings between Ranges
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
mean-method Lists of Atomic Vectors in Natural and Rle Form
mean-method Rle objects
median-method Lists of Atomic Vectors in Natural and Rle Form
median-method Rle objects
members Grouping objects
members-method Grouping objects
mendoapply Endomorphisms via application of a function over an object's elements
mendoapply-method Sequence objects
mendoapply-method Simple and Compressed List Classes
mendoapply-method Endomorphisms via application of a function over an object's elements
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
mseqapply Apply function and cast to Sequence

-- N --

na.exclude DataTable objects
na.exclude-method DataTable objects
na.omit DataTable objects
na.omit-method DataTable 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 XVectorList 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 XVectorList objects
narrow Ranges utility functions
narrow-method Ranges utility functions
narrow-method RangesList utility functions
narrow-method XVectorList objects
nchar-method Lists of Atomic Vectors in Natural and Rle Form
nchar-method Rle objects
NCOL-method DataTable objects
ncol-method External Data Frame
ncol-method List of DataFrames
ncol-method Data on ranges
nearest Nearest neighbor finding
nearest-method Nearest neighbor finding
newViews Views objects
ngap GappedRanges objects
ngap-method GappedRanges objects
nir_list MaskCollection objects
nir_list-method MaskCollection objects
nlevels-method Sequence 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 DataTable objects
NROW-method Sequence 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 Ranges objects
Ops-method List of Ranges
Ops-method Rle objects
order Ranges comparison
order-method Ranges comparison
overlap Interval Search Trees

-- P --

Partitioning Grouping objects
Partitioning-class Grouping objects
PartitioningByEnd Grouping objects
PartitioningByEnd-class Grouping objects
PartitioningByWidth Grouping objects
PartitioningByWidth-class Grouping objects
paste Rle objects
paste-method Rle objects
pgap Set operations on IRanges objects
pgap-method Set operations on IRanges objects
pintersect Set operations on IRanges objects
pintersect-method Set operations on IRanges objects
pmax Rle objects
pmax-method Lists of Atomic Vectors in Natural and Rle Form
pmax-method Rle objects
pmax.int Rle objects
pmax.int-method Lists of Atomic Vectors in Natural and Rle Form
pmax.int-method Rle objects
pmin Rle objects
pmin-method Lists of Atomic Vectors in Natural and Rle Form
pmin-method Rle objects
pmin.int Rle objects
pmin.int-method Lists of Atomic Vectors in Natural and Rle Form
pmin.int-method Rle objects
Position-method Sequence objects
precede Nearest neighbor finding
precede-method Nearest neighbor finding
psetdiff Set operations on IRanges objects
psetdiff-method Set operations on IRanges objects
punion Set operations on IRanges objects
punion-method Set operations on IRanges objects

-- Q --

quantile-method Lists of Atomic Vectors in Natural and Rle Form
quantile-method Rle objects
queryHits Matchings between Ranges
queryHits-method Matchings between Ranges
queryHits-method List of Matchings between Ranges

-- R --

range-method RangedData utility functions
range-method Ranges utility functions
range-method RangesList utility functions
RangedData Data on ranges
rangedData Applying over spaces
RangedData-class Data on ranges
rangedData-method Applying over spaces
RangedData-utils RangedData utility functions
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 Data on ranges
Ranges-class Ranges objects
Ranges-comparison Ranges comparison
ranges-method Data on ranges
ranges-method Selection of ranges and columns
ranges-method Matchings between Ranges
ranges-method List of Matchings between Ranges
Ranges-utils Ranges utility functions
ranges<- Data on ranges
ranges<--method Data on ranges
ranges<--method Selection of ranges and columns
RangesList List of Ranges
RangesList-class List of Ranges
RangesList-utils RangesList utility functions
RangesMatching-class Matchings between Ranges
RangesMatchingList-class List of Matchings between Ranges
RangesORmissing-class Ranges objects
rank-method Ranges comparison
RawList Lists of Atomic Vectors in Natural and Rle Form
RawList-class Lists of Atomic Vectors in Natural and Rle Form
rbind DataTable objects
rbind-method External Data Frame
rbind-method List of DataFrames
rbind-method DataTable objects
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 Ranges utility functions
Reduce-method Sequence objects
reduce-method Data on ranges
reduce-method Ranges utility functions
reduce-method RangesList utility functions
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 Ranges utility functions
reflect-method Ranges utility functions
rep-method Rle objects
rep-method Sequence objects
rep.int Sequence objects
rep.int-method Rle objects
rep.int-method Sequence objects
resize Ranges utility functions
resize-method Ranges utility functions
resize-method RangesList utility functions
restrict Ranges utility functions
restrict-method Ranges utility functions
restrict-method RangesList utility functions
rev-method Rle objects
rev-method Sequence objects
reverse Reverse an IRanges object
reverse-method Reverse an IRanges object
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
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 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 Rle objects
runValue<- Rle objects
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 Low-level string utilities
sapply-method Sequence objects
score Score accessor and setter
score-method Alignments between sequences
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
seqapply Apply function and cast to Sequence
seqselect Sequence objects
seqselect-method External Data Frame
seqselect-method DataTable objects
seqselect-method GappedRanges objects
seqselect-method IRanges and NormalIRanges objects
seqselect-method Data on ranges
seqselect-method Rle objects
seqselect-method Sequence objects
seqselect-method Simple and Compressed List Classes
seqselect-method XVector objects
seqselect-method XVectorList objects
seqselect<- Sequence objects
seqselect<--method Lists of Atomic Vectors in Natural and Rle Form
seqselect<--method DataTable objects
seqselect<--method IRanges and NormalIRanges objects
seqselect<--method Data on ranges
seqselect<--method Rle objects
seqselect<--method Sequence objects
seqselect<--method Simple and Compressed List Classes
seqsplit Apply function and cast to Sequence
Sequence Sequence objects
Sequence-class Sequence objects
setdiff-method Set operations on IRanges objects
setdiff-method RangesList utility functions
shift Ranges utility functions
shift-method Ranges utility functions
shift-method RangesList utility functions
shiftApply Sequence objects
shiftApply-method Rle objects
shiftApply-method Sequence objects
show-method Lists of Atomic Vectors in Natural and Rle Form
show-method List of DataFrames
show-method DataTable objects
show-method GappedRanges objects
show-method Grouping objects
show-method List of IRanges and NormalIRanges
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
show-method Simple and Compressed List Classes
show-method The XIntegerViews class
show-method XVector objects
show-method XVectorList objects
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
simplify Applying over spaces
simplify-method Applying over spaces
simplify<- Applying over spaces
simplify<--method Applying over spaces
slice Utility functions and numeric summary of Views of numerics
slice-method Utility functions and numeric summary of Views of numerics
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 Lists of Atomic Vectors in Natural and Rle Form
sort-method Ranges comparison
sort-method Rle objects
space List of Ranges
space-method Data on ranges
space-method List of Ranges
space-method List of Matchings between Ranges
split-method External Data Frame
split-method List of IRanges and NormalIRanges
split-method Data on ranges
split-method List of Ranges
split-method Rle objects
SplitDataFrameList List of DataFrames
SplitDataFrameList-class List of DataFrames
splitRanges Rle objects
splitRanges-method Rle objects
stack-method List of DataFrames
stack-method Lists of RangedData
stack-method Sequence objects
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 Trees
start-method Data on ranges
start-method Ranges objects
start-method List of Ranges
start-method Rle objects
start<- Ranges objects
start<--method IRanges and NormalIRanges objects
start<--method Data on ranges
start<--method List of Ranges
strsplitAsListOfIntegerVectors Low-level string utilities
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 Matchings between Ranges
subjectHits-method Matchings between Ranges
subjectHits-method List of Matchings between Ranges
subseq XVector objects
subseq-method MaskCollection objects
subseq-method XVector objects
subseq-method XVectorList objects
subseq<- XVector objects
subseq<--method XVector objects
subset-method DataTable objects
subset-method Sequence objects
subsetByOverlaps Interval Search Trees
subsetByOverlaps-method Interval Search Trees
substr-method Rle objects
substring-method Rle objects
subviews Views objects
subviews-method Views objects
successiveIRanges IRanges utility functions
successiveViews Views objects
Summary-method Lists of Atomic Vectors in Natural and Rle Form
Summary-method Rle objects
summary-method List of IRanges and NormalIRanges
summary-method Rle objects
svn.time Low-level string utilities

-- T --

t-method Matchings between Ranges
t-method List of Matchings between Ranges
table Rle objects
table-method Lists of Atomic Vectors in Natural and Rle Form
table-method Rle objects
tail-method DataTable objects
tail-method Sequence objects
tapply-method Sequence objects
threebands Ranges utility functions
threebands-method Ranges utility functions
threebands-method XVectorList 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 Sequence

-- U --

union-method Set operations on IRanges objects
union-method RangesList utility functions
unique-method Lists of Atomic Vectors in Natural and Rle Form
unique-method Ranges comparison
unique-method Rle objects
universe List of Ranges
universe-method Data on ranges
universe-method List of Ranges
universe<- List of Ranges
universe<--method Data on ranges
universe<--method List of Ranges
unlist-method List of IRanges and NormalIRanges
unlist-method Lists of RangedData
unlist-method Ranges objects
unlist-method Simple and Compressed List Classes
update-method IRanges and NormalIRanges objects
update-method Ranges objects
updateObject Update an IRanges object from BioC 2.4 to current version
updateObject-method Update an IRanges object from BioC 2.4 to current version

-- V --

values Sequence objects
values-method Data on ranges
values-method Sequence objects
values<- Sequence objects
values<--method Data on ranges
values<--method Sequence objects
var-method Lists of Atomic Vectors in Natural and Rle Form
var-method Rle objects
viewApply Utility functions and numeric summary of Views of numerics
viewApply-method Utility functions and numeric summary of Views of numerics
viewMaxs Utility functions and numeric summary of Views of numerics
viewMaxs-method Utility functions and numeric summary of Views of numerics
viewMeans Utility functions and numeric summary of Views of numerics
viewMeans-method Utility functions and numeric summary of Views of numerics
viewMins Utility functions and numeric summary of Views of numerics
viewMins-method Utility functions and numeric summary of Views of numerics
viewRangeMaxs Utility functions and numeric summary of Views of numerics
viewRangeMaxs-method Utility functions and numeric summary of Views of numerics
viewRangeMins Utility functions and numeric summary of Views of numerics
viewRangeMins-method Utility functions and numeric summary of Views of numerics
Views Views objects
views Views objects
Views-class Views objects
Views-method The RleViews class
Views-method List of RleViews
Views-method The XIntegerViews class
Views-utils Utility functions and numeric summary of Views of numerics
viewSums Utility functions and numeric summary of Views of numerics
viewSums-method Utility functions and numeric summary of Views of numerics
viewWhichMaxs Utility functions and numeric summary of Views of numerics
viewWhichMaxs-method Utility functions and numeric summary of Views of numerics
viewWhichMins Utility functions and numeric summary of Views of numerics
viewWhichMins-method Utility functions and numeric summary of Views of numerics
vmembers Grouping objects
vmembers-method Grouping objects

-- W --

which-method Lists of Atomic Vectors in Natural and Rle Form
which-method Rle objects
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 MaskCollection objects
width-method Data on ranges
width-method Ranges objects
width-method List of Ranges
width-method Rle objects
width-method XVectorList objects
width<- Ranges objects
width<--method IRanges and NormalIRanges objects
width<--method Data on ranges
width<--method List of Ranges
window-method DataTable objects
window-method GappedRanges objects
window-method IRanges and NormalIRanges objects
window-method Rle objects
window-method Sequence objects
window-method XVector objects
window-method XVectorList objects
window<--method DataTable objects
window<--method Data on ranges
window<--method Sequence objects
with-method Sequence objects
within-method Data on ranges

-- X --

XDouble XVector objects
XDouble-class XVector objects
XInteger XVector objects
XInteger-class XVector objects
XIntegerViews The XIntegerViews class
XIntegerViews-class The XIntegerViews class
XNumeric XVector objects
XRaw XVector objects
XRaw-class XVector objects
XRawList XVectorList objects
XRawList-class XVectorList objects
xtabs-method Statistical modeling with DataTable
XVector XVector objects
XVector-class XVector objects
XVectorList XVectorList objects
XVectorList-class XVectorList objects

-- misc --

[-method External Data Frame
[-method List of DataFrames
[-method Collection of Filter Rules
[-method GappedRanges objects
[-method IRanges and NormalIRanges objects
[-method List of IRanges and NormalIRanges
[-method MaskCollection objects
[-method Data on ranges
[-method Ranges objects
[-method List of Ranges
[-method Rle objects
[-method Sequence objects
[-method Simple and Compressed List Classes
[-method XVector objects
[-method XVectorList objects
[<--method External Data Frame
[<--method List of DataFrames
[<--method IRanges and NormalIRanges objects
[<--method Data on ranges
[<--method Rle objects
[<--method Sequence objects
[<--method XVectorList objects
[[-method External Data Frame
[[-method GappedRanges objects
[[-method Grouping objects
[[-method List of IRanges and NormalIRanges
[[-method MaskCollection objects
[[-method Data on ranges
[[-method Ranges objects
[[-method Sequence objects
[[-method Simple and Compressed List Classes
[[-method Views objects
[[-method XVectorList objects
[[<--method External Data Frame
[[<--method Collection of Filter Rules
[[<--method Data on ranges
[[<--method Simple and Compressed List Classes
[[<--method XVectorList objects