!,Rle-method |
Rle objects |
!= |
Ranges comparison |
!=,integer,XIntegerViews-method |
The XIntegerViews class |
!=,integer,XRleIntegerViews-method |
The XRleIntegerViews class |
!=,Ranges,Ranges-method |
Ranges comparison |
!=,Sequence,Sequence-method |
Sequence objects |
!=,XInteger,XIntegerViews-method |
The XIntegerViews class |
!=,XIntegerViews,integer-method |
The XIntegerViews class |
!=,XIntegerViews,XInteger-method |
The XIntegerViews class |
!=,XIntegerViews,XIntegerViews-method |
The XIntegerViews class |
!=,XRleInteger,XRleIntegerViews-method |
The XRleIntegerViews class |
!=,XRleIntegerViews,integer-method |
The XRleIntegerViews class |
!=,XRleIntegerViews,XRleInteger-method |
The XRleIntegerViews class |
!=,XRleIntegerViews,XRleIntegerViews-method |
The XRleIntegerViews class |
$,RangedData-method |
Data on ranges |
$,TypedList-method |
Typed Lists |
$<-,RangedData-method |
Data on ranges |
$<-,TypedList-method |
Typed Lists |
%in%,Ranges,Ranges-method |
Interval Search Trees |
%in%,Rle,ANY-method |
Rle objects |
*,Ranges,numeric-method |
IRanges utility functions |
< |
Ranges comparison |
<,Ranges,Ranges-method |
Ranges comparison |
<= |
Ranges comparison |
<=,Ranges,Ranges-method |
Ranges comparison |
== |
Ranges comparison |
==,integer,XIntegerViews-method |
The XIntegerViews class |
==,integer,XRleIntegerViews-method |
The XRleIntegerViews class |
==,Ranges,Ranges-method |
Ranges comparison |
==,XInteger,XInteger-method |
Sequence objects |
==,XInteger,XIntegerViews-method |
The XIntegerViews class |
==,XIntegerViews,integer-method |
The XIntegerViews class |
==,XIntegerViews,XInteger-method |
The XIntegerViews class |
==,XIntegerViews,XIntegerViews-method |
The XIntegerViews class |
==,XNumeric,XNumeric-method |
Sequence objects |
==,XRle,XRle-method |
Sequence objects |
==,XRleInteger,XRleIntegerViews-method |
The XRleIntegerViews class |
==,XRleIntegerViews,integer-method |
The XRleIntegerViews class |
==,XRleIntegerViews,XRleInteger-method |
The XRleIntegerViews class |
==,XRleIntegerViews,XRleIntegerViews-method |
The XRleIntegerViews class |
> |
Ranges comparison |
>,Ranges,Ranges-method |
Ranges comparison |
>= |
Ranges comparison |
>=,Ranges,Ranges-method |
Ranges comparison |
active |
MaskCollection objects |
active,FilterRules-method |
Collection of Filter Rules |
active,MaskCollection-method |
MaskCollection objects |
active<-,FilterRules-method |
Collection of Filter Rules |
active<-,MaskCollection-method |
MaskCollection objects |
aggregate,Rle-method |
Rle objects |
AnnotatedList |
Annotated Lists |
AnnotatedList-class |
Annotated Lists |
append,FilterRules,FilterRules-method |
Collection of Filter Rules |
append,MaskCollection,MaskCollection-method |
MaskCollection objects |
append,TypedList,TypedList-method |
Typed Lists |
applyFun |
Applying over spaces |
applyFun,RDApplyParams-method |
Applying over spaces |
applyFun<-,RDApplyParams-method |
Applying over spaces |
applyParams |
Applying over spaces |
applyParams,RDApplyParams-method |
Applying over spaces |
applyParams<-,RDApplyParams-method |
Applying over spaces |
Arith,integer,XRleInteger-method |
Sequence objects |
Arith,XRleInteger,integer-method |
Sequence objects |
Arith,XRleInteger,XRleInteger-method |
Sequence objects |
as.character,Rle-method |
Rle objects |
as.complex,Rle-method |
Rle objects |
as.data.frame,RangedData-method |
Data on ranges |
as.data.frame,Ranges-method |
Ranges objects |
as.data.frame,RangesList-method |
List of Ranges |
as.data.frame,SplitXDataFrameList-method |
List of XDataFrames |
as.data.frame,XDataFrame-method |
External Data Frame |
as.factor,Rle-method |
Rle objects |
as.integer,Rle-method |
Rle objects |
as.integer,XInteger-method |
Sequence objects |
as.integer,XIntegerViews-method |
The XIntegerViews class |
as.integer,XRaw-method |
Sequence objects |
as.integer,XRleInteger-method |
Sequence objects |
as.integer,XRleIntegerViews-method |
The XRleIntegerViews class |
as.list,TypedList-method |
Typed Lists |
as.list,XDataFrame-method |
External Data Frame |
as.logical,Rle-method |
Rle objects |
as.matrix,Ranges-method |
Ranges objects |
as.matrix,RangesMatching-method |
Matchings between Ranges |
as.matrix,RangesMatchingList-method |
List of Matchings between Ranges |
as.numeric,Rle-method |
Rle objects |
as.numeric,XNumeric-method |
Sequence objects |
as.numeric,XSequence-method |
Sequence objects |
as.raw,Rle-method |
Rle objects |
as.table,RangesMatching-method |
Matchings between Ranges |
as.table,RangesMatchingList-method |
List of Matchings between Ranges |
as.vector,Rle,missing-method |
Rle objects |
as.vector,XInteger,missing-method |
Sequence objects |
as.vector,XNumeric,missing-method |
Sequence objects |
as.vector,XRleInteger,missing-method |
Sequence objects |
asNormalIRanges |
IRanges utility functions |
c,FilterRules-method |
Collection of Filter Rules |
c,IRanges-method |
IRanges and NormalIRanges objects |
c,RangedData-method |
Data on ranges |
c,Rle-method |
Rle objects |
c,TypedList-method |
Typed Lists |
c,XRaw-method |
Sequence objects |
cbind |
External Data Frame |
cbind,XDataFrame-method |
External Data Frame |
CharacterList |
Lists of Atomic Vectors in Natural and Rle Form |
CharacterList-class |
Lists of Atomic Vectors in Natural and Rle Form |
chartr,ANY,ANY,Rle-method |
Rle objects |
class:IRanges |
IRanges and NormalIRanges objects |
class:MaskCollection |
MaskCollection objects |
class:NormalIRanges |
IRanges and NormalIRanges objects |
class:Ranges |
Ranges objects |
class:Rle |
Rle objects |
class:RleViews |
The RleViews class |
class:Sequence |
Sequence objects |
class:Views |
Views objects |
class:XInteger |
Sequence objects |
class:XIntegerViews |
The XIntegerViews class |
class:XNumeric |
Sequence objects |
class:XRaw |
Sequence objects |
class:XRle |
Sequence objects |
class:XRleInteger |
Sequence objects |
class:XRleIntegerViews |
The XRleIntegerViews class |
class:XSequence |
Sequence objects |
coerce,ANY,XDataFrame-method |
External Data Frame |
coerce,data.frame,XDataFrame-method |
External Data Frame |
coerce,factor,Rle-method |
Rle objects |
coerce,integer,XDataFrame-method |
External Data Frame |
coerce,integer,XInteger-method |
Sequence objects |
coerce,integer,XRleInteger-method |
Sequence objects |
coerce,integer,XSequence-method |
Sequence objects |
coerce,IntervalTree,IRanges-method |
Interval Search Trees |
coerce,IRanges,IntervalTree-method |
Interval Search Trees |
coerce,IRanges,NormalIRanges-method |
IRanges utility functions |
coerce,IRangesList,list-method |
List of IRanges |
coerce,IRangesList,NormalIRanges-method |
List of IRanges |
coerce,list,XDataFrame-method |
External Data Frame |
coerce,MaskCollection,NormalIRanges-method |
MaskCollection objects |
coerce,matrix,XDataFrame-method |
External Data Frame |
coerce,numeric,XNumeric-method |
Sequence objects |
coerce,numeric,XSequence-method |
Sequence objects |
coerce,RangedData,XDataFrame-method |
Data on ranges |
coerce,Ranges,IntervalTree-method |
Interval Search Trees |
coerce,RangesList,IRangesList-method |
List of Ranges |
coerce,RangesList,RangedData-method |
List of Ranges |
coerce,Rle,character-method |
Rle objects |
coerce,Rle,complex-method |
Rle objects |
coerce,Rle,factor-method |
Rle objects |
coerce,Rle,integer-method |
Rle objects |
coerce,Rle,IRanges-method |
Rle objects |
coerce,Rle,logical-method |
Rle objects |
coerce,Rle,numeric-method |
Rle objects |
coerce,Rle,RangedData-method |
Data on ranges |
coerce,Rle,raw-method |
Rle objects |
coerce,Rle,vector-method |
Rle objects |
coerce,SplitXDataFrameList,XDataFrame-method |
List of XDataFrames |
coerce,TypedList,list-method |
Typed Lists |
coerce,vector,Rle-method |
Rle objects |
coerce,Views,NormalIRanges-method |
Views objects |
coerce,XDataFrame,data.frame-method |
External Data Frame |
coerce,XRle,RangedData-method |
Data on ranges |
Complex,Rle-method |
Rle objects |
ComplexList |
Lists of Atomic Vectors in Natural and Rle Form |
ComplexList-class |
Lists of Atomic Vectors in Natural and Rle Form |
cor,Rle,Rle-method |
Rle objects |
cov,Rle,Rle-method |
Rle objects |
coverage |
Coverage across a set of ranges |
coverage,IRanges-method |
Coverage across a set of ranges |
coverage,MaskCollection-method |
Coverage across a set of ranges |
IntegerList |
Lists of Atomic Vectors in Natural and Rle Form |
IntegerList-class |
Lists of Atomic Vectors in Natural and Rle Form |
intersect,IRanges,IRanges-method |
Set operations on IRanges objects |
IntervalTree |
Interval Search Trees |
IntervalTree-class |
Interval Search Trees |
intToAdjacentRanges |
IRanges utility functions |
intToRanges |
IRanges utility functions |
IRanges |
IRanges and NormalIRanges objects |
IRanges-class |
IRanges and NormalIRanges objects |
IRanges-setops |
Set operations on IRanges objects |
IRanges-utils |
IRanges utility functions |
IRangesList |
List of IRanges |
IRangesList-class |
List of IRanges |
is.array,XDataFrame-method |
External Data Frame |
is.na,Rle-method |
Rle objects |
isDisjoint |
Ranges objects |
isDisjoint,Ranges-method |
Ranges objects |
isEmpty |
Ranges objects |
isEmpty,MaskCollection-method |
MaskCollection objects |
isEmpty,NormalIRanges-method |
IRanges and NormalIRanges objects |
isEmpty,Ranges-method |
Ranges objects |
isEmpty,TypedList-method |
Typed Lists |
isNormal |
Ranges objects |
isNormal,Ranges-method |
Ranges objects |
names,IRanges-method |
IRanges and NormalIRanges objects |
names,MaskCollection-method |
MaskCollection objects |
names,RangedData-method |
Data on ranges |
names,TypedList-method |
Typed Lists |
names<-,IRanges-method |
IRanges and NormalIRanges objects |
names<-,MaskCollection-method |
MaskCollection objects |
names<-,RangedData-method |
Data on ranges |
names<-,TypedList-method |
Typed Lists |
narrow |
IRanges utility functions |
narrow,IRanges-method |
IRanges utility functions |
narrow,NormalIRanges-method |
IRanges utility functions |
narrow,Views-method |
Views objects |
nchar,Rle-method |
Rle objects |
nearest |
Nearest neighbor finding |
nearest,Ranges,RangesORmissing-method |
Nearest neighbor finding |
newViews |
Views objects |
nir_list |
MaskCollection objects |
nir_list,MaskCollection-method |
MaskCollection objects |
NormalIRanges |
IRanges and NormalIRanges objects |
NormalIRanges-class |
IRanges and NormalIRanges objects |
nrun |
Rle objects |
nrun,Rle-method |
Rle objects |
NumericList |
Lists of Atomic Vectors in Natural and Rle Form |
NumericList-class |
Lists of Atomic Vectors in Natural and Rle Form |
pgap |
Set operations on IRanges objects |
pgap,IRanges,IRanges-method |
Set operations on IRanges objects |
pintersect |
Set operations on IRanges objects |
pintersect,IRanges,IRanges-method |
Set operations on IRanges objects |
pmax |
Rle objects |
pmax,Rle-method |
Rle objects |
pmax.int |
Rle objects |
pmax.int,Rle-method |
Rle objects |
pmin |
Rle objects |
pmin,Rle-method |
Rle objects |
pmin.int |
Rle objects |
pmin.int,Rle-method |
Rle objects |
precede |
Nearest neighbor finding |
precede,Ranges,RangesORmissing-method |
Nearest neighbor finding |
psetdiff |
Set operations on IRanges objects |
psetdiff,IRanges,IRanges-method |
Set operations on IRanges objects |
punion |
Set operations on IRanges objects |
punion,IRanges,IRanges-method |
Set operations on IRanges objects |
range,RangedData-method |
RangedData utility functions |
range,Ranges-method |
IRanges utility functions |
range,RangesList-method |
RangesList utility functions |
RangedData |
Data on ranges |
rangedData |
Applying over spaces |
rangedData,RDApplyParams-method |
Applying over spaces |
RangedData-class |
Data on ranges |
RangedData-utils |
RangedData utility functions |
rangedData<-,RDApplyParams-method |
Applying over spaces |
RangedDataList |
Lists of RangedData |
RangedDataList-class |
Lists of RangedData |
Ranges |
Ranges objects |
ranges |
Data on ranges |
ranges,RangedData-method |
Data on ranges |
ranges,RangesMatching-method |
Matchings between Ranges |
ranges,RangesMatchingList-method |
List of Matchings between Ranges |
Ranges-class |
Ranges objects |
Ranges-comparison |
Ranges comparison |
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 |
Ranges comparison |
rank,Ranges-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 |
External Data Frame |
rbind,RangedData-method |
Data on ranges |
rbind,XDataFrame-method |
External Data Frame |
rdapply |
Applying over spaces |
rdapply,RDApplyParams-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 |
IRanges utility functions |
reduce,IRanges-method |
IRanges utility functions |
reduce,MaskCollection-method |
MaskCollection objects |
reduce,RangesList-method |
RangesList utility functions |
reduce,XRanges-method |
External Ranges |
reducerFun |
Applying over spaces |
reducerFun,RDApplyParams-method |
Applying over spaces |
reducerFun<-,RDApplyParams-method |
Applying over spaces |
reducerParams |
Applying over spaces |
reducerParams,RDApplyParams-method |
Applying over spaces |
reducerParams<-,RDApplyParams-method |
Applying over spaces |
reflect |
IRanges utility functions |
reflect,Ranges-method |
IRanges utility functions |
rep,Ranges-method |
Ranges objects |
rep,Rle-method |
Rle objects |
rep,Sequence-method |
Sequence objects |
rep,XRle-method |
Sequence objects |
rep.int |
Rle objects |
rep.int,Rle-method |
Rle objects |
restrict |
IRanges utility functions |
restrict,IRanges-method |
IRanges utility functions |
restrict,Views-method |
Views objects |
rev,Rle-method |
Rle objects |
reverse |
Reverse ranges |
reverse,IRanges-method |
Reverse ranges |
reverse,MaskCollection-method |
Reverse ranges |
reverse,NormalIRanges-method |
Reverse ranges |
reverse,XRle-method |
Sequence objects |
Rle |
Rle objects |
Rle,missing,missing-method |
Rle objects |
Rle,vectorORfactor,integer-method |
Rle objects |
Rle,vectorORfactor,missing-method |
Rle objects |
Rle,vectorORfactor,numeric-method |
Rle objects |
Rle-class |
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 |
runLength |
Rle objects |
runLength,Rle-method |
Rle objects |
runLength<-,Rle-method |
Rle objects |
runValue |
Rle objects |
runValue,Rle-method |
Rle objects |
runValue<-,Rle-method |
Rle objects |
score |
Alignments between sequences |
score,AlignmentSpace-method |
Alignments between sequences |
sd,Rle-method |
Rle objects |
Sequence |
Sequence objects |
Sequence-class |
Sequence objects |
setdiff,IRanges,IRanges-method |
Set operations on IRanges objects |
shift |
IRanges utility functions |
shift,IRanges-method |
IRanges utility functions |
shiftApply |
Rle objects |
shiftApply,Rle,Rle-method |
Rle objects |
show,MaskCollection-method |
MaskCollection objects |
show,RangedData-method |
Data on ranges |
show,Ranges-method |
Ranges objects |
show,RangesList-method |
List of Ranges |
show,Rle-method |
Rle objects |
show,RleViews-method |
The RleViews class |
show,TypedList-method |
Typed Lists |
show,XDataFrame-method |
External Data Frame |
show,XIntegerViews-method |
The XIntegerViews class |
show,XNumeric-method |
Sequence objects |
show,XRleInteger-method |
Sequence objects |
show,XRleIntegerViews-method |
The XRleIntegerViews class |
show,XSequence-method |
Sequence objects |
simplify |
Applying over spaces |
simplify,RDApplyParams-method |
Applying over spaces |
simplify<-,RDApplyParams-method |
Applying over spaces |
slice |
Utility functions and numeric summary of Views of numerics |
slice,integer-method |
Utility functions and numeric summary of Views of numerics |
slice,Rle-method |
Utility functions and numeric summary of Views of numerics |
slice,XInteger-method |
Utility functions and numeric summary of Views of numerics |
slice,XRleInteger-method |
Utility functions and numeric summary of Views of numerics |
solveUserSEW |
The SEW (Start/End/Width) interface |
sort |
Ranges comparison |
sort,Ranges-method |
Ranges comparison |
sort,Rle-method |
Rle objects |
space |
List of Ranges |
space,RangedData-method |
Data on ranges |
space,RangesList-method |
List of Ranges |
space,RangesMatchingList-method |
List of Matchings between Ranges |
split,RangedData-method |
Data on ranges |
split,Ranges-method |
List of Ranges |
split,XDataFrame-method |
External Data Frame |
SplitXDataFrameList |
List of XDataFrames |
SplitXDataFrameList-class |
List of XDataFrames |
start,IRanges-method |
IRanges and NormalIRanges objects |
start,RangedData-method |
Data on ranges |
start,Ranges-method |
Ranges objects |
start,RangesList-method |
List of Ranges |
start,Rle-method |
Rle objects |
start,XRanges-method |
External Ranges |
start<-,IRanges-method |
IRanges and NormalIRanges objects |
sub,ANY,ANY,Rle-method |
Rle objects |
subject |
Views objects |
subject,Views-method |
Views objects |
subseq |
Sequence objects |
subseq,MaskCollection-method |
MaskCollection objects |
subseq,Rle-method |
Rle objects |
subseq,Sequence-method |
Sequence objects |
subseq,vector-method |
Sequence objects |
subseq,XRle-method |
Sequence objects |
subseq,XSequence-method |
Sequence objects |
subseq<-,ANY-method |
Sequence objects |
substr,Rle-method |
Rle objects |
substring,Rle-method |
Rle objects |
subviews |
Views objects |
subviews,Views-method |
Views objects |
successiveIRanges |
IRanges utility functions |
successiveViews |
Views objects |
summary,IRangesList-method |
List of IRanges |
Summary,Rle-method |
Rle objects |
summary,Rle-method |
Rle objects |
values |
Data on ranges |
values,RangedData-method |
Data on ranges |
var,Rle,missing-method |
Rle objects |
var,Rle,Rle-method |
Rle objects |
viewApply |
Utility functions and numeric summary of Views of numerics |
viewApply,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewApply,Views-method |
Utility functions and numeric summary of Views of numerics |
viewMaxs |
Utility functions and numeric summary of Views of numerics |
viewMaxs,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewMaxs,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewMaxs,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewMins |
Utility functions and numeric summary of Views of numerics |
viewMins,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewMins,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewMins,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewRangeMaxs |
Utility functions and numeric summary of Views of numerics |
viewRangeMaxs,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewRangeMins |
Utility functions and numeric summary of Views of numerics |
viewRangeMins,RleViews-method |
Utility functions and numeric summary of Views of numerics |
Views |
Views objects |
views |
Views objects |
Views,integer-method |
The XIntegerViews class |
Views,Rle-method |
The RleViews class |
Views,XInteger-method |
The XIntegerViews class |
Views,XRleInteger-method |
The XRleIntegerViews class |
Views-class |
Views objects |
Views-utils |
Utility functions and numeric summary of Views of numerics |
viewSums |
Utility functions and numeric summary of Views of numerics |
viewSums,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewSums,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewSums,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMaxs |
Utility functions and numeric summary of Views of numerics |
viewWhichMaxs,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMaxs,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMaxs,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMins |
Utility functions and numeric summary of Views of numerics |
viewWhichMins,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMins,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMins,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |