| !,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 |
| $,ListLike-method |
ListLike objects |
| $,RangedData-method |
Data on ranges |
| $<-,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<- |
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<- |
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 |
| 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,Ranges-method |
Ranges objects |
| as.integer,Rle-method |
Rle objects |
| as.integer,XInteger-method |
Sequence objects |
| as.integer,XRaw-method |
Sequence objects |
| as.integer,XRleInteger-method |
Sequence objects |
| as.list,ListLike-method |
ListLike objects |
| 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.raw,XRaw-method |
Sequence 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,XRaw,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:ListLike |
ListLike 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,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,logical,IRanges-method |
IRanges and NormalIRanges objects |
| coerce,logical,NormalIRanges-method |
IRanges and NormalIRanges objects |
| coerce,MaskCollection,NormalIRanges-method |
MaskCollection objects |
| coerce,matrix,XDataFrame-method |
External Data Frame |
| coerce,numeric,XInteger-method |
Sequence objects |
| coerce,numeric,XNumeric-method |
Sequence objects |
| coerce,numeric,XRaw-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,raw,XRaw-method |
Sequence objects |
| coerce,raw,XSequence-method |
Sequence 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,Sequence,Views-method |
Views 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 |
| coverage,numeric-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 |
| 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<- |
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 |
| 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<- |
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,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 objects |
| runLength<-,Rle-method |
Rle objects |
| runValue |
Rle objects |
| runValue,Rle-method |
Rle objects |
| runValue<- |
Rle objects |
| runValue<-,Rle-method |
Rle objects |
| sapply |
ListLike objects |
| sapply,ListLike-method |
ListLike objects |
| sapply,TypedList-method |
Typed Lists |
| 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<- |
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 IRanges constructor and supporting functions |
| solveUserSEW0 |
The IRanges constructor and supporting functions |
| 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<- |
Ranges objects |
| 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<- |
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 |