active |
MaskCollection objects |
active,FilterRules-method |
Collection of Filter Rules |
active,MaskCollection-method |
MaskCollection objects |
active<- |
MaskCollection objects |
active<-,FilterRules-method |
Collection of Filter Rules |
active<-,MaskCollection-method |
MaskCollection objects |
aggregate,CompressedList-method |
Simple and Compressed List Classes |
aggregate,data.frame-method |
Sequence objects |
aggregate,DataTable-method |
DataTable objects |
aggregate,matrix-method |
Sequence objects |
aggregate,Rle-method |
Rle objects |
aggregate,Sequence-method |
Sequence objects |
aggregate,SimpleList-method |
Simple and Compressed List Classes |
aggregate,ts-method |
Sequence objects |
aggregate,vector-method |
Sequence objects |
Annotated |
Annotated class |
Annotated-class |
Annotated class |
append,FilterRules,FilterRules-method |
Collection of Filter Rules |
append,MaskCollection,MaskCollection-method |
MaskCollection objects |
append,Sequence,Sequence-method |
Sequence objects |
applyFun |
Applying over spaces |
applyFun,RDApplyParams-method |
Applying over spaces |
applyFun<- |
Applying over spaces |
applyFun<-,RDApplyParams-method |
Applying over spaces |
applyParams |
Applying over spaces |
applyParams,RDApplyParams-method |
Applying over spaces |
applyParams<- |
Applying over spaces |
applyParams<-,RDApplyParams-method |
Applying over spaces |
as.character,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.character,Rle-method |
Rle objects |
as.complex,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.complex,Rle-method |
Rle objects |
as.data.frame,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.data.frame,DataFrame-method |
External Data Frame |
as.data.frame,GroupedIRanges-method |
XVectorList 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,SplitDataFrameList-method |
List of DataFrames |
as.env |
Sequence objects |
as.env,DataTable-method |
DataTable objects |
as.env,RangedData-method |
Data on ranges |
as.env,Sequence-method |
Sequence objects |
as.factor,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.factor,Rle-method |
Rle objects |
as.integer,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.integer,Ranges-method |
Ranges objects |
as.integer,Rle-method |
Rle objects |
as.integer,XInteger-method |
XVector objects |
as.integer,XRaw-method |
XVector objects |
as.list,CompressedList-method |
Simple and Compressed List Classes |
as.list,Sequence-method |
Sequence objects |
as.list,SimpleList-method |
Simple and Compressed List Classes |
as.logical,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
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,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.numeric,Rle-method |
Rle objects |
as.numeric,XDouble-method |
XVector objects |
as.numeric,XVector-method |
XVector objects |
as.raw,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.raw,Rle-method |
Rle objects |
as.raw,XRaw-method |
XVector objects |
as.table,RangesMatching-method |
Matchings between Ranges |
as.table,RangesMatchingList-method |
List of Matchings between Ranges |
as.vector,AtomicList,missing-method |
Lists of Atomic Vectors in Natural and Rle Form |
as.vector,Rle,missing-method |
Rle objects |
as.vector,XDouble,missing-method |
XVector objects |
as.vector,XInteger,missing-method |
XVector objects |
as.vector,XRaw,missing-method |
XVector objects |
asNormalIRanges |
IRanges utility functions |
AtomicList-class |
Lists of Atomic Vectors in Natural and Rle Form |
c,CompressedList-method |
Simple and Compressed List Classes |
c,FilterRules-method |
Collection of Filter Rules |
c,GroupedIRanges-method |
XVectorList objects |
c,IRanges-method |
IRanges and NormalIRanges objects |
c,RangedData-method |
Data on ranges |
c,Rle-method |
Rle objects |
c,Sequence-method |
Sequence objects |
c,SimpleList-method |
Simple and Compressed List Classes |
c,XRaw-method |
XVector objects |
c,XVectorList-method |
XVectorList objects |
cbind |
DataTable objects |
cbind,DataFrame-method |
External Data Frame |
cbind,DataFrameList-method |
List of DataFrames |
cbind,DataTable-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,ANY,ANY,Rle-method |
Rle objects |
class:Binning |
Grouping objects |
class:DataTable |
DataTable objects |
class:Dups |
Grouping objects |
class:GroupedIRanges |
XVectorList objects |
class:Grouping |
Grouping objects |
class:H2LGrouping |
Grouping objects |
class:IRanges |
IRanges and NormalIRanges objects |
class:MaskCollection |
MaskCollection objects |
class:NormalIRanges |
IRanges and NormalIRanges objects |
class:Partitioning |
Grouping objects |
class:PartitioningByEnd |
Grouping objects |
class:PartitioningByWidth |
Grouping objects |
class:Ranges |
Ranges objects |
class:Rle |
Rle objects |
class:RleViews |
The RleViews class |
class:Sequence |
Sequence objects |
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,ANY,CompressedSplitDataFrameList-method |
List of DataFrames |
coerce,ANY,SimpleSplitDataFrameList-method |
List of DataFrames |
coerce,AtomicList,character-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,complex-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,CompressedSplitDataFrameList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,data.frame-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,factor-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,integer-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,logical-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,numeric-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,raw-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,SimpleSplitDataFrameList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,AtomicList,vector-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,character,Rle-method |
Rle objects |
coerce,complex,Rle-method |
Rle objects |
coerce,data.frame,DataFrame-method |
External Data Frame |
coerce,data.frame,RangedData-method |
Data on ranges |
coerce,DataFrame,data.frame-method |
External Data Frame |
coerce,DataTable,RangedData-method |
Data on ranges |
coerce,factor,Rle-method |
Rle objects |
coerce,integer,DataFrame-method |
External Data Frame |
coerce,integer,IRanges-method |
IRanges and NormalIRanges objects |
coerce,integer,Rle-method |
Rle objects |
coerce,integer,XVector-method |
XVector 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,logical,IRanges-method |
IRanges and NormalIRanges objects |
coerce,logical,NormalIRanges-method |
IRanges and NormalIRanges objects |
coerce,logical,Rle-method |
Rle objects |
coerce,LogicalList,CompressedIRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,LogicalList,IRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,LogicalList,SimpleIRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,MaskCollection,NormalIRanges-method |
MaskCollection objects |
coerce,matrix,DataFrame-method |
External Data Frame |
coerce,numeric,IRanges-method |
IRanges and NormalIRanges objects |
coerce,numeric,Rle-method |
Rle objects |
coerce,numeric,XDouble-method |
XVector objects |
coerce,numeric,XInteger-method |
XVector objects |
coerce,numeric,XRaw-method |
XVector objects |
coerce,numeric,XVector-method |
XVector objects |
coerce,RangedData,DataFrame-method |
Data on ranges |
coerce,Ranges,IntervalTree-method |
Interval Search Trees |
coerce,Ranges,IRanges-method |
IRanges and NormalIRanges objects |
coerce,Ranges,PartitioningByEnd-method |
Grouping objects |
coerce,Ranges,PartitioningByWidth-method |
Grouping objects |
coerce,Ranges,RangedData-method |
Data on ranges |
coerce,RangesList,CompressedIRangesList-method |
List of Ranges |
coerce,RangesList,RangedData-method |
List of Ranges |
coerce,RangesList,SimpleIRangesList-method |
List of Ranges |
coerce,raw,Rle-method |
Rle objects |
coerce,raw,XRaw-method |
XVector objects |
coerce,raw,XVector-method |
XVector objects |
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,NormalIRanges-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,RleList,CompressedIRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,RleList,IRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,RleList,RangedData-method |
Data on ranges |
coerce,RleList,SimpleIRangesList-method |
Lists of Atomic Vectors in Natural and Rle Form |
coerce,Sequence,DataFrame-method |
External Data Frame |
coerce,Sequence,list-method |
Sequence objects |
coerce,Sequence,Views-method |
Views objects |
coerce,SplitDataFrameList,DataFrame-method |
List of DataFrames |
coerce,vector,DataFrame-method |
External Data Frame |
coerce,vector,Rle-method |
Rle objects |
coerce,Views,NormalIRanges-method |
Views objects |
collapse |
MaskCollection objects |
collapse,MaskCollection-method |
MaskCollection objects |
colnames,DataFrame-method |
External Data Frame |
colnames,DataFrameList-method |
List of DataFrames |
colnames,RangedData-method |
Data on ranges |
colnames<-,CompressedSplitDataFrameList-method |
List of DataFrames |
colnames<-,DataFrame-method |
External Data Frame |
colnames<-,RangedData-method |
Data on ranges |
colnames<-,SimpleDataFrameList-method |
List of DataFrames |
Complex,CompressedAtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
Complex,Rle-method |
Rle objects |
Complex,SimpleAtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
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-class |
List of IRanges |
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 |
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,Rle,Rle-method |
Rle objects |
countOverlap |
Interval Search Trees |
countOverlaps |
Interval Search Trees |
countOverlaps,Ranges,Ranges-method |
Interval Search Trees |
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 |
coverage,numeric-method |
Coverage across a set of ranges |
coverage,RangedData-method |
Coverage across a set of ranges |
coverage,RangesList-method |
Coverage across a set of ranges |
coverage,Views-method |
Coverage across a set of ranges |
coverage.getShift0FromStartEnd |
Coverage across a set of ranges |
coverage.getWidthFromStartEnd |
Coverage across a set of ranges |
coverage.isCalledWithStartEndInterface |
Coverage across a set of ranges |
coverage.normargWidth |
Coverage across a set of ranges |
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<- |
Applying over spaces |
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 |
ranges<- |
Data on ranges |
ranges<-,RangedData-method |
Data on ranges |
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-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,DataFrame-method |
External Data Frame |
rbind,DataFrameList-method |
List of DataFrames |
rbind,DataTable-method |
DataTable objects |
rbind,RangedData-method |
Data on ranges |
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,ANY,Sequence-method |
Sequence objects |
reduce,IRanges-method |
IRanges utility functions |
reduce,RangedData-method |
Data on ranges |
reduce,Ranges-method |
IRanges utility functions |
reduce,RangesList-method |
RangesList utility functions |
reducerFun |
Applying over spaces |
reducerFun,RDApplyParams-method |
Applying over spaces |
reducerFun<- |
Applying over spaces |
reducerFun<-,RDApplyParams-method |
Applying over spaces |
reducerParams |
Applying over spaces |
reducerParams,RDApplyParams-method |
Applying over spaces |
reducerParams<- |
Applying over spaces |
reducerParams<-,RDApplyParams-method |
Applying over spaces |
reflect |
IRanges utility functions |
reflect,Ranges-method |
IRanges utility functions |
rep,Rle-method |
Rle objects |
rep,Sequence-method |
Sequence objects |
rep.int |
Rle objects |
rep.int,Rle-method |
Rle objects |
resize |
IRanges utility functions |
resize,CompressedIRangesList-method |
RangesList utility functions |
resize,IRanges-method |
IRanges utility functions |
resize,NormalIRanges-method |
IRanges utility functions |
resize,Ranges-method |
IRanges utility functions |
resize,RangesList-method |
RangesList utility functions |
restrict |
IRanges utility functions |
restrict,CompressedIRangesList-method |
RangesList utility functions |
restrict,IRanges-method |
IRanges utility functions |
restrict,Ranges-method |
IRanges utility functions |
restrict,RangesList-method |
RangesList utility functions |
rev,Rle-method |
Rle objects |
rev,Sequence-method |
Sequence objects |
reverse |
Reverse an IRanges object |
reverse,IRanges-method |
Reverse an IRanges object |
reverse,MaskCollection-method |
Reverse an IRanges object |
reverse,NormalIRanges-method |
Reverse an IRanges object |
reverse,SharedRaw-method |
Reverse an IRanges object |
reverse,SharedVector_Pool-method |
Reverse an IRanges object |
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 |
RleViewsList |
List of RleViews |
RleViewsList-class |
List of RleViews |
rownames,DataFrame-method |
External Data Frame |
rownames,DataFrameList-method |
List of DataFrames |
rownames,RangedData-method |
Data on ranges |
rownames<-,CompressedSplitDataFrameList-method |
List of DataFrames |
rownames<-,DataFrame-method |
External Data Frame |
rownames<-,RangedData-method |
Data on ranges |
rownames<-,SimpleDataFrameList-method |
List of DataFrames |
runLength |
Rle objects |
runLength,Rle-method |
Rle objects |
runLength<- |
Rle objects |
runLength<-,Rle-method |
Rle objects |
runmean |
Fixed width running window summaries across vector-like objects |
runmean,Rle-method |
Rle objects |
runmean,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
runmed,Rle-method |
Rle objects |
runmed,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
runq |
Fixed width running window summaries across vector-like objects |
runq,Rle-method |
Rle objects |
runq,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
runstat |
Fixed width running window summaries across vector-like objects |
runsum |
Fixed width running window summaries across vector-like objects |
runsum,Rle-method |
Rle objects |
runsum,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
runValue |
Rle objects |
runValue,Rle-method |
Rle objects |
runValue<- |
Rle objects |
runValue<-,Rle-method |
Rle objects |
runwtsum |
Fixed width running window summaries across vector-like objects |
runwtsum,Rle-method |
Rle objects |
runwtsum,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
safeExplode |
Low-level string utilities |
sapply,Sequence-method |
Sequence objects |
score |
Score accessor and setter |
score,AlignmentSpace-method |
Alignments between sequences |
score,RangedData-method |
Data on ranges |
score<- |
Score accessor and setter |
score<-,RangedData-method |
Data on ranges |
sd,Rle-method |
Rle objects |
seqextract |
Sequence objects |
seqselect |
Sequence objects |
seqselect,CompressedList-method |
Simple and Compressed List Classes |
seqselect,DataTable-method |
DataTable objects |
seqselect,GroupedIRanges-method |
XVectorList objects |
seqselect,IRanges-method |
IRanges and NormalIRanges objects |
seqselect,RangedData-method |
Data on ranges |
seqselect,Rle-method |
Rle objects |
seqselect,Sequence-method |
Sequence objects |
seqselect,SimpleList-method |
Simple and Compressed List Classes |
seqselect,vector-method |
Sequence objects |
seqselect,XVector-method |
XVector objects |
seqselect,XVectorList-method |
XVectorList objects |
seqselect<- |
Sequence objects |
seqselect<-,CompressedAtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
seqselect<-,CompressedList-method |
Simple and Compressed List Classes |
seqselect<-,DataTable-method |
DataTable objects |
seqselect<-,RangedData-method |
Data on ranges |
seqselect<-,Rle-method |
Rle objects |
seqselect<-,Sequence-method |
Sequence objects |
seqselect<-,SimpleAtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
seqselect<-,SimpleList-method |
Simple and Compressed List Classes |
seqselect<-,vector-method |
Sequence objects |
Sequence |
Sequence objects |
Sequence-class |
Sequence objects |
setdiff,IRanges,IRanges-method |
Set operations on IRanges objects |
setdiff,RangesList,RangesList-method |
RangesList utility functions |
shift |
IRanges utility functions |
shift,CompressedIRangesList-method |
RangesList utility functions |
shift,IRanges-method |
IRanges utility functions |
shift,Ranges-method |
IRanges utility functions |
shift,RangesList-method |
RangesList utility functions |
shiftApply |
Sequence objects |
shiftApply,Rle,Rle-method |
Rle objects |
shiftApply,Sequence,Sequence-method |
Sequence objects |
shiftApply,vector,vector-method |
Sequence objects |
show,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
show,CompressedList-method |
Simple and Compressed List Classes |
show,DataTable-method |
DataTable objects |
show,Dups-method |
Grouping objects |
show,GroupedIRanges-method |
XVectorList objects |
show,Grouping-method |
Grouping objects |
show,IRangesList-method |
List of Ranges |
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,RleList-method |
Lists of Atomic Vectors in Natural and Rle Form |
show,RleViews-method |
The RleViews class |
show,SimpleList-method |
Simple and Compressed List Classes |
show,SplitDataFrameList-method |
List of DataFrames |
show,XDouble-method |
XVector objects |
show,XIntegerViews-method |
The XIntegerViews class |
show,XVector-method |
XVector 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-class |
List of IRanges |
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 |
SimpleNumericList |
Lists of Atomic Vectors in Natural and Rle Form |
SimpleNumericList-class |
Lists of Atomic Vectors in Natural and Rle Form |
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,RDApplyParams-method |
Applying over spaces |
simplify<- |
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,RleList-method |
Utility functions and numeric summary of Views of numerics |
slice,XInteger-method |
Utility functions and numeric summary of Views of numerics |
smoothEnds,Rle-method |
Rle objects |
solveUserSEW |
The IRanges constructor and supporting functions |
solveUserSEW0 |
The IRanges constructor and supporting functions |
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,DataFrame-method |
External Data Frame |
split,IRanges-method |
List of Ranges |
split,RangedData-method |
Data on ranges |
split,Ranges-method |
List of Ranges |
split,Rle-method |
Rle objects |
SplitDataFrameList |
List of DataFrames |
SplitDataFrameList-class |
List of DataFrames |
start,CompressedIRangesList-method |
List of Ranges |
start,IntervalTree-method |
Interval Search Trees |
start,IRanges-method |
IRanges and NormalIRanges objects |
start,PartitioningByEnd-method |
Grouping objects |
start,PartitioningByWidth-method |
Grouping objects |
start,RangedData-method |
Data on ranges |
start,Ranges-method |
Ranges objects |
start,RangesList-method |
List of Ranges |
start,Rle-method |
Rle objects |
start<- |
Ranges objects |
start<-,IRanges-method |
IRanges and NormalIRanges objects |
start<-,RangedData-method |
Data on ranges |
start<-,RangesList-method |
List of Ranges |
strsplitAsListOfIntegerVectors |
Low-level string utilities |
sub,ANY,ANY,Rle-method |
Rle objects |
subject |
Views objects |
subject,SimpleRleViewsList-method |
List of RleViews |
subject,Views-method |
Views objects |
subjectHits |
Matchings between Ranges |
subjectHits,RangesMatching-method |
Matchings between Ranges |
subjectHits,RangesMatchingList-method |
List of Matchings between Ranges |
subseq |
XVector objects |
subseq,MaskCollection-method |
MaskCollection objects |
subseq,XVector-method |
XVector objects |
subseq<- |
XVector objects |
subseq<-,XVector-method |
XVector objects |
subset,DataTable-method |
DataTable objects |
subset,Sequence-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,AtomicList-method |
Lists of Atomic Vectors in Natural and Rle Form |
summary,CompressedIRangesList-method |
List of IRanges |
Summary,Rle-method |
Rle objects |
summary,Rle-method |
Rle objects |
union,IRanges,IRanges-method |
Set operations on IRanges objects |
union,RangesList,RangesList-method |
RangesList utility functions |
unique,Ranges-method |
Ranges comparison |
unique,Rle-method |
Rle objects |
universe |
List of Ranges |
universe,RangedData-method |
Data on ranges |
universe,RangesList-method |
List of Ranges |
universe<- |
List of Ranges |
universe<-,RangedData-method |
Data on ranges |
universe<-,RangesList-method |
List of Ranges |
unlist,CompressedList-method |
Simple and Compressed List Classes |
unlist,IRangesList-method |
List of IRanges |
unlist,RangedDataList-method |
Lists of RangedData |
unlist,Ranges-method |
Ranges objects |
unlist,SimpleList-method |
Simple and Compressed List Classes |
update,IRanges-method |
IRanges and NormalIRanges objects |
update,Ranges-method |
Ranges objects |
updateObject |
Update an IRanges object from BioC 2.4 to current version |
updateObject,AnnotatedList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,ANY-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,CharacterList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,ComplexList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,FilterRules-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,IntegerList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,IntervalTree-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,IRanges-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,IRangesList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,LogicalList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,MaskCollection-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,NormalIRanges-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,NumericList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RangedData-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RangedDataList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RangesList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RangesMatchingList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RawList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RDApplyParams-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,Rle-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RleList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,RleViews-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,SplitXDataFrameList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,XDataFrame-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,XDataFrameList-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,XIntegerViews-method |
Update an IRanges object from BioC 2.4 to current version |
updateObject,XVector-method |
Update an IRanges object from BioC 2.4 to current version |
values |
Data on ranges |
values,RangedData-method |
Data on ranges |
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,RleViewsList-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,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewMaxs,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
viewMeans |
Utility functions and numeric summary of Views of numerics |
viewMeans,RleViews-method |
Utility functions and numeric summary of Views of numerics |
viewMeans,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewMeans,XIntegerViews-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,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewMins,XIntegerViews-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 |
viewRangeMaxs,RleViewsList-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 |
viewRangeMins,RleViewsList-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,RleList-method |
List of RleViews |
Views,XInteger-method |
The XIntegerViews 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,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewSums,XIntegerViews-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,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMaxs,XIntegerViews-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,RleViewsList-method |
Utility functions and numeric summary of Views of numerics |
viewWhichMins,XIntegerViews-method |
Utility functions and numeric summary of Views of numerics |
vmembers |
Grouping objects |
vmembers,Grouping-method |
Grouping objects |
vmembers,H2LGrouping-method |
Grouping objects |