| !=,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 |