!=,integer,XIntegerViews-method |
The XIntegerViews class |
!=,integer,XRleIntegerViews-method |
The XRleIntegerViews class |
!=,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 |
%in%,Ranges,Ranges-method |
Interval Search Trees |
==,integer,XIntegerViews-method |
The XIntegerViews class |
==,integer,XRleIntegerViews-method |
The XRleIntegerViews class |
==,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 |
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 |
annotation |
Data on ranges |
annotation,RangedData-method |
Data on ranges |
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.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,SplitXDataFrame-method |
Split XDataFrame |
as.data.frame,XDataFrame-method |
External Data Frame |
as.integer,XInteger-method |
Sequence objects |
as.integer,XIntegerViews-method |
The XIntegerViews class |
as.integer,XRleInteger-method |
Sequence objects |
as.integer,XRleIntegerViews-method |
The XRleIntegerViews class |
as.list,TypedList-method |
Typed Lists |
as.matrix,Ranges-method |
Ranges objects |
as.matrix,RangesMatching-method |
Matchings between Ranges |
as.numeric,XNumeric-method |
Sequence objects |
as.table,RangesMatching-method |
Matchings between Ranges |
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,GenomicData-method |
Data on a Genome |
c,IRanges-method |
IRanges and NormalIRanges objects |
c,RangedData-method |
Data on ranges |
c,TypedList-method |
Typed Lists |
cbind |
External Data Frame |
cbind,XDataFrame-method |
External Data Frame |
chrom |
Data on a Genome |
chrom,GenomicData-method |
Data on a Genome |
class:IRanges |
IRanges and NormalIRanges objects |
class:MaskCollection |
MaskCollection objects |
class:NormalIRanges |
IRanges and NormalIRanges objects |
class:Ranges |
Ranges objects |
class:Sequence |
Sequence objects |
class:SequenceORvector |
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,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,NormalIRanges-method |
List of IRanges |
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,SplitXDataFrame,XDataFrame-method |
Split XDataFrame |
coerce,TypedList,list-method |
Typed Lists |
coerce,Views,NormalIRanges-method |
Views objects |
coerce,XDataFrame,data.frame-method |
External Data Frame |
coerce,XRle,GenomicData-method |
Data on a Genome |
coerce,XRle,RangedData-method |
Data on ranges |
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 |
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-class |
Ranges objects |
RangesList |
List of Ranges |
RangesList-class |
List of Ranges |
RangesList-utils |
RangesList utility functions |
RangesMatching-class |
Matchings between Ranges |
rbind |
External Data Frame |
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 |
rep,Ranges-method |
Ranges objects |
rep,Sequence-method |
Sequence objects |
rep,XRle-method |
Sequence objects |
restrict |
IRanges utility functions |
restrict,IRanges-method |
IRanges utility functions |
restrict,Views-method |
Views objects |
reverse |
Reverse ranges |
reverse,IRanges-method |
Reverse ranges |
reverse,MaskCollection-method |
Reverse ranges |
reverse,NormalIRanges-method |
Reverse ranges |
reverse,XRle-method |
Sequence objects |
Sequence |
Sequence objects |
Sequence-class |
Sequence objects |
SequenceORvector |
Sequence objects |
SequenceORvector-class |
Sequence objects |
setdiff,IRanges,IRanges-method |
Set operations on IRanges objects |
shift |
IRanges utility functions |
shift,IRanges-method |
IRanges utility functions |
show,MaskCollection-method |
MaskCollection objects |
show,RangedData-method |
Data on ranges |
show,Ranges-method |
Ranges objects |
show,RangesList-method |
List of Ranges |
show,TypedList-method |
Typed Lists |
show,XDataFrame-method |
External Data Frame |
show,XInteger-method |
Sequence objects |
show,XIntegerViews-method |
The XIntegerViews class |
show,XNumeric-method |
Sequence objects |
show,XRleInteger-method |
Sequence objects |
show,XRleIntegerViews-method |
The XRleIntegerViews class |
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,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 |
split,RangedData-method |
Data on ranges |
split,Ranges-method |
List of Ranges |
split,XDataFrame-method |
External Data Frame |
SplitXDataFrame |
Split XDataFrame |
SplitXDataFrame-class |
Split XDataFrame |
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,XRanges-method |
External Ranges |
start<-,IRanges-method |
IRanges and NormalIRanges objects |
strand |
Data on a Genome |
strand,GenomicData-method |
Data on a Genome |
strand,missing-method |
Data on a Genome |
subject |
Views objects |
subject,Views-method |
Views objects |
subseq |
Sequence objects |
subseq,MaskCollection-method |
MaskCollection objects |
subseq,SequenceORvector-method |
Sequence objects |
subseq,XSequence-method |
Sequence objects |
subviews |
Views objects |
subviews,Views-method |
Views objects |
successiveIRanges |
IRanges utility functions |
successiveViews |
Views objects |
summary,RangesList-method |
List of Ranges |
values |
Data on ranges |
values,RangedData-method |
Data on ranges |
viewMaxs |
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,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewMins,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
Views |
Views objects |
views |
Views objects |
Views,integer-method |
The XIntegerViews 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,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewSums,XRleIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
[,FilterRules,ANY,ANY,ANY-method |
Collection of Filter Rules |
[,IRanges,ANY,ANY,ANY-method |
IRanges and NormalIRanges objects |
[,MaskCollection,ANY,ANY,ANY-method |
MaskCollection objects |
[,RangedData,ANY,ANY,ANY-method |
Data on ranges |
[,TypedList,ANY,ANY,ANY-method |
Typed Lists |
[,XDataFrame,ANY,ANY,ANY-method |
External Data Frame |
[,XInteger,ANY,ANY,ANY-method |
Sequence objects |
[,XNumeric,ANY,ANY,ANY-method |
Sequence objects |
[,XRle,ANY,ANY,ANY-method |
Sequence objects |
[<-,MaskCollection,ANY,ANY,ANY-method |
MaskCollection objects |
[<-,RangedData,ANY,ANY,ANY-method |
Data on ranges |
[<-,Ranges,ANY,ANY,ANY-method |
Ranges objects |
[<-,Sequence,ANY,ANY,ANY-method |
Sequence objects |
[<-,TypedList,ANY,ANY,ANY-method |
Typed Lists |
[[,MaskCollection-method |
MaskCollection objects |
[[,RangedData-method |
Data on ranges |
[[,TypedList-method |
Typed Lists |
[[,Views-method |
Views objects |
[[,XDataFrame-method |
External Data Frame |
[[,XIntegerViews-method |
The XIntegerViews class |
[[,XRleIntegerViews-method |
The XRleIntegerViews class |
[[<-,FilterRules-method |
Collection of Filter Rules |
[[<-,MaskCollection-method |
MaskCollection objects |
[[<-,RangedData-method |
Data on ranges |
[[<-,TypedList-method |
Typed Lists |
[[<-,Views-method |
Views objects |
[[<-,XDataFrame-method |
External Data Frame |
[[<-,XIntegerViews-method |
The XIntegerViews class |
[[<-,XRleIntegerViews-method |
The XRleIntegerViews class |