1067 lines
46 KiB
Plaintext
1067 lines
46 KiB
Plaintext
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!,CompressedList-method CompressedList-class
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%outside% findOverlaps-methods
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%over% findOverlaps-methods
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%within% findOverlaps-methods
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active MaskCollection-class
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active,MaskCollection-method MaskCollection-class
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active<- MaskCollection-class
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active<-,MaskCollection-method MaskCollection-class
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all,CompressedAtomicList-method AtomicList-utils
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all,CompressedRleList-method AtomicList-utils
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any,CompressedAtomicList-method AtomicList-utils
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anyNA,CompressedAtomicList-method AtomicList-utils
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append,MaskCollection,MaskCollection-method MaskCollection-class
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as.character,IPosRanges-method IPosRanges-class
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as.data.frame,IPos-method IPos-class
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as.data.frame,IPosRanges-method IPosRanges-class
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as.data.frame.IPos IPos-class
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as.data.frame.IPosRanges IPosRanges-class
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as.env,SDFLWrapperForTransform-method DataFrameList-class
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as.factor,IPosRanges-method IPosRanges-class
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as.list,CompressedAtomicList-method AtomicList-class
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as.list,CompressedNormalIRangesList-method IRangesList-class
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as.list,Hits-method Hits-class-leftovers
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as.list,SortedByQueryHits-method Hits-class-leftovers
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as.matrix,AtomicList-method AtomicList-class
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as.matrix,CompressedHitsList-method CompressedHitsList-class
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as.matrix,IPosRanges-method IPosRanges-class
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as.matrix,Views-method Views-class
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as.matrix,ViewsList-method ViewsList-class
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as.vector,AtomicList-method AtomicList-class
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asNormalIRanges IRanges-utils
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AtomicList AtomicList-class
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AtomicList-class AtomicList-class
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AtomicList-utils AtomicList-utils
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bindROWS,CompressedList-method CompressedList-class
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bindROWS,IPos-method IPos-class
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bindROWS,NCList-method NCList-class
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bindROWS,Partitioning-method Grouping-class
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bindROWS,Views-method Views-class
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breakInChunks IRanges-utils
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cbind,DataFrameList-method DataFrameList-class
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CharacterList AtomicList-class
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CharacterList-class AtomicList-class
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chartr,ANY,ANY,CompressedCharacterList-method AtomicList-utils
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chartr,ANY,ANY,CompressedRleList-method AtomicList-utils
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chartr,ANY,ANY,SimpleCharacterList-method AtomicList-utils
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chartr,ANY,ANY,SimpleRleList-method AtomicList-utils
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class:AtomicList AtomicList-class
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class:CharacterList AtomicList-class
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class:ComplexList AtomicList-class
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class:CompressedAtomicList AtomicList-class
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class:CompressedCharacterList AtomicList-class
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class:CompressedComplexList AtomicList-class
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class:CompressedDataFrameList DataFrameList-class
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class:CompressedDFrameList DataFrameList-class
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class:CompressedFactorList AtomicList-class
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class:CompressedGrouping Grouping-class
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class:CompressedHitsList CompressedHitsList-class
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class:CompressedIntegerList AtomicList-class
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class:CompressedIRangesList IRangesList-class
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class:CompressedList CompressedList-class
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class:CompressedLogicalList AtomicList-class
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class:CompressedManyToManyGrouping Grouping-class
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class:CompressedManyToOneGrouping Grouping-class
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class:CompressedNormalIRangesList IRangesList-class
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class:CompressedNumericList AtomicList-class
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class:CompressedRawList AtomicList-class
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class:CompressedRleList AtomicList-class
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class:CompressedSplitDataFrameList DataFrameList-class
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class:CompressedSplitDFrameList DataFrameList-class
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class:DataFrameList DataFrameList-class
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class:DFrameList DataFrameList-class
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class:Dups Grouping-class
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class:FactorList AtomicList-class
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class:Grouping Grouping-class
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class:GroupingIRanges Grouping-class
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class:GroupingRanges Grouping-class
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class:H2LGrouping Grouping-class
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class:IntegerList AtomicList-class
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class:IntegerRanges IntegerRanges-class
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class:IntegerRangesList IntegerRangesList-class
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class:IntegerRanges_OR_missing nearest-methods
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class:IPos IPos-class
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class:IPosRanges IPosRanges-class
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class:IRanges IRanges-class
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class:IRangesList IRangesList-class
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class:LogicalList AtomicList-class
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class:ManyToManyGrouping Grouping-class
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class:ManyToOneGrouping Grouping-class
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class:MaskCollection MaskCollection-class
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class:NCList NCList-class
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class:NCLists NCList-class
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class:NormalIRanges IRanges-class
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class:NormalIRangesList IRangesList-class
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class:NumericList AtomicList-class
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class:Partitioning Grouping-class
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class:PartitioningByEnd Grouping-class
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class:PartitioningByWidth Grouping-class
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class:PartitioningMap Grouping-class
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class:RawList AtomicList-class
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class:RleList AtomicList-class
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class:RleViews RleViews-class
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class:SimpleAtomicList AtomicList-class
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class:SimpleCharacterList AtomicList-class
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class:SimpleComplexList AtomicList-class
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class:SimpleDataFrameList DataFrameList-class
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class:SimpleDFrameList DataFrameList-class
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class:SimpleFactorList AtomicList-class
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class:SimpleGrouping Grouping-class
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class:SimpleIntegerList AtomicList-class
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class:SimpleIntegerRangesList IntegerRangesList-class
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class:SimpleIRangesList IRangesList-class
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class:SimpleLogicalList AtomicList-class
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class:SimpleManyToManyGrouping Grouping-class
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class:SimpleManyToOneGrouping Grouping-class
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class:SimpleNormalIRangesList IRangesList-class
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class:SimpleNumericList AtomicList-class
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class:SimpleRawList AtomicList-class
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class:SimpleRleList AtomicList-class
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class:SimpleSplitDataFrameList DataFrameList-class
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class:SimpleSplitDFrameList DataFrameList-class
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class:SimpleViewsList ViewsList-class
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class:SplitDataFrameList DataFrameList-class
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class:SplitDFrameList DataFrameList-class
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class:StitchedIPos IPos-class
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class:UnstitchedIPos IPos-class
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class:Views Views-class
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class:ViewsList ViewsList-class
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classNameForDisplay,CompressedDFrameList-method DataFrameList-class
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classNameForDisplay,CompressedList-method CompressedList-class
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classNameForDisplay,SimpleDFrameList-method DataFrameList-class
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coerce,ANY,CompressedDataFrameList-method DataFrameList-class
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coerce,ANY,CompressedList-method CompressedList-class
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coerce,ANY,CompressedSplitDataFrameList-method DataFrameList-class
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coerce,ANY,CompressedSplitDFrameList-method DataFrameList-class
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coerce,ANY,DataFrameList-method DataFrameList-class
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coerce,ANY,IntegerRanges-method IRanges-class
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coerce,ANY,IPos-method IPos-class
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coerce,ANY,SimpleDataFrameList-method DataFrameList-class
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coerce,ANY,SimpleSplitDataFrameList-method DataFrameList-class
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coerce,ANY,SimpleSplitDFrameList-method DataFrameList-class
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coerce,ANY,SplitDataFrameList-method DataFrameList-class
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coerce,ANY,SplitDFrameList-method DataFrameList-class
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coerce,ANY,StitchedIPos-method IPos-class
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coerce,ANY,UnstitchedIPos-method IPos-class
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coerce,ANY,vector-method IRanges-internals
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coerce,AtomicList,CharacterList-method AtomicList-class
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coerce,AtomicList,ComplexList-method AtomicList-class
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coerce,AtomicList,IntegerList-method AtomicList-class
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coerce,AtomicList,LogicalList-method AtomicList-class
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coerce,AtomicList,NumericList-method AtomicList-class
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coerce,AtomicList,RawList-method AtomicList-class
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coerce,AtomicList,RleList-method AtomicList-class
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coerce,AtomicList,RleViews AtomicList-class
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coerce,character,IRanges-method IRanges-class
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coerce,CompressedAtomicList,list-method AtomicList-class
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coerce,CompressedIRangesList,CompressedNormalIRangesList-method IRangesList-class
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coerce,CompressedRleList,CompressedIRangesList-method IRangesList-class
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coerce,DataFrame,Grouping-method Grouping-class
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coerce,DataFrame,SplitDFrameList-method DataFrameList-class
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coerce,DataFrameList,DFrame-method DataFrameList-class
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coerce,factor,IRanges-method IRanges-class
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coerce,FactorList,Grouping-method Grouping-class
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coerce,grouping,Grouping-method Grouping-class
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coerce,grouping,ManyToOneGrouping-method Grouping-class
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coerce,Hits,CompressedIntegerList-method Hits-class-leftovers
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coerce,Hits,Grouping Hits-class-leftovers
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coerce,Hits,Grouping-method Grouping-class
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coerce,Hits,IntegerList-method Hits-class-leftovers
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coerce,Hits,List-method Hits-class-leftovers
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coerce,integer,IRanges-method IRanges-class
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coerce,integer,NormalIRanges-method IRanges-class
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coerce,IntegerRanges,CompressedIRangesList-method IRangesList-class
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coerce,IntegerRanges,IPos-method IPos-class
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coerce,IntegerRanges,IRanges-method IRanges-class
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coerce,IntegerRanges,NCList-method NCList-class
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coerce,IntegerRanges,PartitioningByEnd-method Grouping-class
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coerce,IntegerRanges,PartitioningByWidth-method Grouping-class
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coerce,IntegerRanges,StitchedIPos-method IPos-class
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coerce,IntegerRanges,UnstitchedIPos-method IPos-class
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coerce,IntegerRangesList,CompressedNormalIRangesList-method IRangesList-class
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coerce,IntegerRangesList,NCLists-method NCList-class
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coerce,IntegerRangesList,NormalIRangesList-method IRangesList-class
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coerce,IntegerRangesList,RangedSelection-method RangedSelection-class
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coerce,IntegerRangesList,SimpleIRangesList-method IRangesList-class
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coerce,IntegerRangesList,SimpleNormalIRangesList-method IRangesList-class
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coerce,IRanges,NormalIRanges-method IRanges-utils
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coerce,List,CompressedIRangesList-method IRangesList-class
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coerce,list,CompressedIRangesList-method IRangesList-class
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coerce,List,CompressedSplitDFrameList-method DataFrameList-class
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coerce,List,IRangesList-method IRangesList-class
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coerce,list,IRangesList-method IRangesList-class
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coerce,List,SimpleIRangesList-method IRangesList-class
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coerce,list,SimpleIRangesList-method IRangesList-class
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coerce,List,SimpleSplitDFrameList-method DataFrameList-class
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coerce,list,SplitDFrameList-method DataFrameList-class
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coerce,logical,IRanges-method IRanges-class
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coerce,logical,NormalIRanges-method IRanges-class
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coerce,LogicalList,CompressedNormalIRangesList-method IRangesList-class
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coerce,LogicalList,NormalIRangesList-method IRangesList-class
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coerce,LogicalList,SimpleNormalIRangesList-method IRangesList-class
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coerce,ManyToOneGrouping,factor-method Grouping-class
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coerce,MaskCollection,NormalIRanges-method MaskCollection-class
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coerce,NCLists,CompressedIRangesList-method NCList-class
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coerce,NCLists,IRangesList-method NCList-class
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coerce,NormalIRangesList,CompressedNormalIRangesList-method IRangesList-class
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coerce,numeric,IRanges-method IRanges-class
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coerce,numeric,NormalIRanges-method IRanges-class
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coerce,Rle,IRanges-method Rle-class-leftovers
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coerce,Rle,NormalIRanges-method Rle-class-leftovers
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coerce,RleList,CompressedNormalIRangesList-method IRangesList-class
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coerce,RleList,NormalIRangesList-method IRangesList-class
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coerce,RleList,SimpleNormalIRangesList-method IRangesList-class
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coerce,RleViewsList,IRangesList-method RleViewsList-class
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coerce,RleViewsList,SimpleIRangesList-method RleViewsList-class
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coerce,SimpleIntegerRangesList,SimpleIRangesList-method IRangesList-class
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coerce,SimpleIRangesList,SimpleNormalIRangesList-method IRangesList-class
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coerce,SimpleList,SimpleIRangesList-method IRangesList-class
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coerce,SimpleList,SplitDFrameList-method DataFrameList-class
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coerce,SortedByQueryHits,CompressedIntegerList-method Hits-class-leftovers
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coerce,SortedByQueryHits,IntegerList-method Hits-class-leftovers
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coerce,SortedByQueryHits,IntegerRanges-method Hits-class-leftovers
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coerce,SortedByQueryHits,IRanges-method Hits-class-leftovers
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coerce,SortedByQueryHits,List-method Hits-class-leftovers
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coerce,SortedByQueryHits,Partitioning-method Hits-class-leftovers
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coerce,SortedByQueryHits,PartitioningByEnd-method Hits-class-leftovers
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coerce,SplitDataFrameList,DFrame-method DataFrameList-class
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coerce,StitchedIPos,UnstitchedIPos-method IPos-class
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coerce,UnstitchedIPos,StitchedIPos-method IPos-class
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coerce,vector,AtomicList-method AtomicList-class
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coerce,vector,CompressedCharacterList-method AtomicList-class
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coerce,vector,CompressedComplexList-method AtomicList-class
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coerce,vector,CompressedIntegerList-method AtomicList-class
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coerce,vector,CompressedLogicalList-method AtomicList-class
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coerce,vector,CompressedNumericList-method AtomicList-class
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coerce,vector,CompressedRawList-method AtomicList-class
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coerce,vector,CompressedRleList-method AtomicList-class
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coerce,vector,Grouping-method Grouping-class
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coerce,vector,ManyToManyGrouping-method Grouping-class
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coerce,vector,ManyToOneGrouping-method Grouping-class
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coerce,vector,SimpleCharacterList-method AtomicList-class
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coerce,vector,SimpleComplexList-method AtomicList-class
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coerce,vector,SimpleIntegerList-method AtomicList-class
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coerce,vector,SimpleLogicalList-method AtomicList-class
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coerce,vector,SimpleNumericList-method AtomicList-class
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coerce,vector,SimpleRawList-method AtomicList-class
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coerce,vector,SimpleRleList-method AtomicList-class
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coerce,Vector,Views-method Views-class
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coerce,Views,IntegerRanges-method Views-class
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coerce,Views,IRanges-method Views-class
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coerce,Views,NormalIRanges-method Views-class
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collapse MaskCollection-class
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collapse,MaskCollection-method MaskCollection-class
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colnames,CompressedSplitDataFrameList-method DataFrameList-class
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colnames,DataFrameList-method DataFrameList-class
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colnames,RangedSelection-method RangedSelection-class
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colnames,SDFLWrapperForTransform-method DataFrameList-class
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colnames,SplitDataFrameList-method DataFrameList-class
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colnames<-,CompressedSplitDataFrameList-method DataFrameList-class
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colnames<-,RangedSelection-method RangedSelection-class
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colnames<-,SimpleDataFrameList-method DataFrameList-class
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columnMetadata DataFrameList-class
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columnMetadata,CompressedSplitDataFrameList-method DataFrameList-class
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columnMetadata,SimpleSplitDataFrameList-method DataFrameList-class
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columnMetadata<- DataFrameList-class
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columnMetadata<-,CompressedSplitDataFrameList-method DataFrameList-class
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columnMetadata<-,SimpleSplitDataFrameList-method DataFrameList-class
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commonColnames DataFrameList-class
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commonColnames,CompressedSplitDataFrameList-method DataFrameList-class
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commonColnames,SimpleSplitDataFrameList-method DataFrameList-class
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commonColnames<- DataFrameList-class
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commonColnames<-,CompressedSplitDataFrameList-method DataFrameList-class
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commonColnames<-,SimpleSplitDataFrameList-method DataFrameList-class
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Complex,AtomicList-method AtomicList-utils
|
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Complex,CompressedAtomicList-method AtomicList-utils
|
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ComplexList AtomicList-class
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ComplexList-class AtomicList-class
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CompressedAtomicList AtomicList-class
|
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CompressedAtomicList-class AtomicList-class
|
||
|
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CompressedCharacterList AtomicList-class
|
||
|
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CompressedCharacterList-class AtomicList-class
|
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|
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CompressedComplexList AtomicList-class
|
||
|
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CompressedComplexList-class AtomicList-class
|
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CompressedDataFrameList DataFrameList-class
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CompressedDataFrameList-class DataFrameList-class
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CompressedDFrameList DataFrameList-class
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CompressedDFrameList-class DataFrameList-class
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CompressedFactorList AtomicList-class
|
||
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CompressedFactorList-class AtomicList-class
|
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CompressedGrouping-class Grouping-class
|
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CompressedHitsList CompressedHitsList-class
|
||
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CompressedHitsList-class CompressedHitsList-class
|
||
|
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CompressedIntegerList AtomicList-class
|
||
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CompressedIntegerList-class AtomicList-class
|
||
|
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CompressedIRangesList IRangesList-class
|
||
|
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CompressedIRangesList-class IRangesList-class
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||
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CompressedList CompressedList-class
|
||
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CompressedList-class CompressedList-class
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||
|
|
CompressedLogicalList AtomicList-class
|
||
|
|
CompressedLogicalList-class AtomicList-class
|
||
|
|
CompressedManyToManyGrouping-class Grouping-class
|
||
|
|
CompressedManyToOneGrouping-class Grouping-class
|
||
|
|
CompressedNormalIRangesList IRangesList-class
|
||
|
|
CompressedNormalIRangesList-class IRangesList-class
|
||
|
|
CompressedNumericList AtomicList-class
|
||
|
|
CompressedNumericList-class AtomicList-class
|
||
|
|
CompressedRawList AtomicList-class
|
||
|
|
CompressedRawList-class AtomicList-class
|
||
|
|
CompressedRleList AtomicList-class
|
||
|
|
CompressedRleList-class AtomicList-class
|
||
|
|
CompressedSplitDataFrameList DataFrameList-class
|
||
|
|
CompressedSplitDataFrameList-class DataFrameList-class
|
||
|
|
CompressedSplitDFrameList DataFrameList-class
|
||
|
|
CompressedSplitDFrameList-class DataFrameList-class
|
||
|
|
cor,AtomicList,AtomicList-method AtomicList-utils
|
||
|
|
countOverlaps findOverlaps-methods
|
||
|
|
countOverlaps,integer,Vector-method findOverlaps-methods
|
||
|
|
countOverlaps,IntegerRanges,IntegerRanges-method findOverlaps-methods
|
||
|
|
countOverlaps,IntegerRangesList,IntegerRangesList-method findOverlaps-methods
|
||
|
|
countOverlaps,Vector,missing-method findOverlaps-methods
|
||
|
|
countOverlaps,Vector,Vector-method findOverlaps-methods
|
||
|
|
cov,AtomicList,AtomicList-method AtomicList-utils
|
||
|
|
coverage coverage-methods
|
||
|
|
coverage,IntegerRanges-method coverage-methods
|
||
|
|
coverage,IntegerRangesList-method coverage-methods
|
||
|
|
coverage,StitchedIPos-method coverage-methods
|
||
|
|
coverage,Views-method coverage-methods
|
||
|
|
coverage-methods coverage-methods
|
||
|
|
cummax,CompressedAtomicList-method AtomicList-utils
|
||
|
|
cummin,CompressedAtomicList-method AtomicList-utils
|
||
|
|
cumprod,CompressedAtomicList-method AtomicList-utils
|
||
|
|
cumsum,CompressedAtomicList-method AtomicList-utils
|
||
|
|
DataFrameList DataFrameList-class
|
||
|
|
DataFrameList-class DataFrameList-class
|
||
|
|
desc MaskCollection-class
|
||
|
|
desc,MaskCollection-method MaskCollection-class
|
||
|
|
desc<- MaskCollection-class
|
||
|
|
desc<-,MaskCollection-method MaskCollection-class
|
||
|
|
DFrameList DataFrameList-class
|
||
|
|
DFrameList-class DataFrameList-class
|
||
|
|
diff,CompressedAtomicList-method AtomicList-utils
|
||
|
|
diff.AtomicList AtomicList-utils
|
||
|
|
dim,DataFrameList-method DataFrameList-class
|
||
|
|
dimnames,DataFrameList-method DataFrameList-class
|
||
|
|
dimnames<-,DataFrameList-method DataFrameList-class
|
||
|
|
dims,DataFrameList-method DataFrameList-class
|
||
|
|
disjoin inter-range-methods
|
||
|
|
disjoin,CompressedIRangesList-method inter-range-methods
|
||
|
|
disjoin,IntegerRanges-method inter-range-methods
|
||
|
|
disjoin,IntegerRangesList-method inter-range-methods
|
||
|
|
disjoin,NormalIRanges-method inter-range-methods
|
||
|
|
disjointBins inter-range-methods
|
||
|
|
disjointBins,IntegerRanges-method inter-range-methods
|
||
|
|
disjointBins,IntegerRangesList-method inter-range-methods
|
||
|
|
disjointBins,NormalIRanges-method inter-range-methods
|
||
|
|
distance nearest-methods
|
||
|
|
distance,IntegerRanges,IntegerRanges-method nearest-methods
|
||
|
|
distance,Pairs,missing-method nearest-methods
|
||
|
|
distanceToNearest nearest-methods
|
||
|
|
distanceToNearest,IntegerRanges,IntegerRanges_OR_missing-method nearest-methods
|
||
|
|
drop,AtomicList-method AtomicList-class
|
||
|
|
duplicated,CompressedAtomicList-method AtomicList-class
|
||
|
|
duplicated,CompressedList-method AtomicList-class
|
||
|
|
duplicated,Dups-method Grouping-class
|
||
|
|
Dups Grouping-class
|
||
|
|
Dups-class Grouping-class
|
||
|
|
elementNROWS,CompressedList-method CompressedList-class
|
||
|
|
elementNROWS,NCLists-method NCList-class
|
||
|
|
elementNROWS,Ranges-method IPosRanges-class
|
||
|
|
end,CompressedRangesList-method IRangesList-class
|
||
|
|
end,NCList-method NCList-class
|
||
|
|
end,NCLists-method NCList-class
|
||
|
|
end,PartitioningByEnd-method Grouping-class
|
||
|
|
end,PartitioningByWidth-method Grouping-class
|
||
|
|
end,Pos-method IPosRanges-class
|
||
|
|
end,Ranges-method IPosRanges-class
|
||
|
|
end,RangesList-method IntegerRangesList-class
|
||
|
|
end,SimpleViewsList-method ViewsList-class
|
||
|
|
end<- IPosRanges-class
|
||
|
|
end<-,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
end<-,IRanges-method IRanges-class
|
||
|
|
end<-,Views-method Views-class
|
||
|
|
endsWith,CharacterList,ANY-method AtomicList-utils
|
||
|
|
endsWith,RleList,ANY-method AtomicList-utils
|
||
|
|
equisplit extractListFragments
|
||
|
|
eval Vector-class-leftovers
|
||
|
|
eval,expression,Vector-method Vector-class-leftovers
|
||
|
|
eval,language,Vector-method Vector-class-leftovers
|
||
|
|
extractList extractList
|
||
|
|
extractList,ANY,ANY-method extractList
|
||
|
|
extractList,ANY-method extractList
|
||
|
|
extractListFragments extractListFragments
|
||
|
|
extractROWS,IPos-method IPos-class
|
||
|
|
extractROWS,NCList,ANY-method NCList-class
|
||
|
|
extractROWS,Partitioning-method Grouping-class
|
||
|
|
FactorList AtomicList-class
|
||
|
|
FactorList-class AtomicList-class
|
||
|
|
findOverlapPairs findOverlaps-methods
|
||
|
|
findOverlaps findOverlaps-methods
|
||
|
|
findOverlaps,ANY,Pairs-method findOverlaps-methods
|
||
|
|
findOverlaps,integer,IntegerRanges-method findOverlaps-methods
|
||
|
|
findOverlaps,IntegerRanges,IntegerRanges-method findOverlaps-methods
|
||
|
|
findOverlaps,IntegerRangesList,IntegerRangesList-method findOverlaps-methods
|
||
|
|
findOverlaps,Pairs,ANY-method findOverlaps-methods
|
||
|
|
findOverlaps,Pairs,missing-method findOverlaps-methods
|
||
|
|
findOverlaps,Pairs,Pairs-method findOverlaps-methods
|
||
|
|
findOverlaps,Vector,missing-method findOverlaps-methods
|
||
|
|
findOverlaps-methods findOverlaps-methods
|
||
|
|
findRange Rle-class-leftovers
|
||
|
|
findRange,Rle-method Rle-class-leftovers
|
||
|
|
flank intra-range-methods
|
||
|
|
flank,Ranges-method intra-range-methods
|
||
|
|
flank,RangesList-method intra-range-methods
|
||
|
|
follow nearest-methods
|
||
|
|
follow,IntegerRanges,IntegerRanges_OR_missing-method nearest-methods
|
||
|
|
from,CompressedHitsList-method CompressedHitsList-class
|
||
|
|
gaps inter-range-methods
|
||
|
|
gaps,CompressedIRangesList-method inter-range-methods
|
||
|
|
gaps,IntegerRanges-method inter-range-methods
|
||
|
|
gaps,IntegerRangesList-method inter-range-methods
|
||
|
|
gaps,MaskCollection-method inter-range-methods
|
||
|
|
gaps,Views-method inter-range-methods
|
||
|
|
getListElement,IPosRanges-method IPosRanges-class
|
||
|
|
Grouping Grouping-class
|
||
|
|
Grouping-class Grouping-class
|
||
|
|
GroupingIRanges Grouping-class
|
||
|
|
GroupingIRanges-class Grouping-class
|
||
|
|
GroupingRanges Grouping-class
|
||
|
|
GroupingRanges-class Grouping-class
|
||
|
|
grouplengths Grouping-class
|
||
|
|
grouplengths,CompressedGrouping-method Grouping-class
|
||
|
|
grouplengths,Grouping-method Grouping-class
|
||
|
|
grouplengths,GroupingRanges-method Grouping-class
|
||
|
|
grouplengths,H2LGrouping-method Grouping-class
|
||
|
|
grouprank Grouping-class
|
||
|
|
grouprank,H2LGrouping-method Grouping-class
|
||
|
|
gsub,ANY,ANY,CompressedCharacterList-method AtomicList-utils
|
||
|
|
gsub,ANY,ANY,CompressedRleList-method AtomicList-utils
|
||
|
|
gsub,ANY,ANY,SimpleCharacterList-method AtomicList-utils
|
||
|
|
gsub,ANY,ANY,SimpleRleList-method AtomicList-utils
|
||
|
|
H2LGrouping Grouping-class
|
||
|
|
H2LGrouping-class Grouping-class
|
||
|
|
high2low Grouping-class
|
||
|
|
high2low,ANY-method Grouping-class
|
||
|
|
high2low,H2LGrouping-method Grouping-class
|
||
|
|
Hits-examples Hits-class-leftovers
|
||
|
|
ifelse2 AtomicList-utils
|
||
|
|
ifelse2,ANY,ANY,List-method AtomicList-utils
|
||
|
|
ifelse2,ANY,List,ANY-method AtomicList-utils
|
||
|
|
ifelse2,CompressedLogicalList,ANY,ANY-method AtomicList-utils
|
||
|
|
ifelse2,CompressedLogicalList,ANY,List-method AtomicList-utils
|
||
|
|
ifelse2,CompressedLogicalList,List,ANY-method AtomicList-utils
|
||
|
|
ifelse2,CompressedLogicalList,List,List-method AtomicList-utils
|
||
|
|
ifelse2,List,ANY,ANY-method AtomicList-utils
|
||
|
|
ifelse2,SimpleLogicalList,ANY,ANY-method AtomicList-utils
|
||
|
|
ifelse2,SimpleLogicalList,ANY,List-method AtomicList-utils
|
||
|
|
ifelse2,SimpleLogicalList,List,ANY-method AtomicList-utils
|
||
|
|
ifelse2,SimpleLogicalList,List,List-method AtomicList-utils
|
||
|
|
INCOMPATIBLE_ARANGES_MSG extractListFragments
|
||
|
|
IntegerList AtomicList-class
|
||
|
|
IntegerList-class AtomicList-class
|
||
|
|
IntegerRanges IntegerRanges-class
|
||
|
|
IntegerRanges-class IntegerRanges-class
|
||
|
|
IntegerRangesList IntegerRangesList-class
|
||
|
|
IntegerRangesList-class IntegerRangesList-class
|
||
|
|
IntegerRanges_OR_missing nearest-methods
|
||
|
|
IntegerRanges_OR_missing-class nearest-methods
|
||
|
|
inter-range-methods inter-range-methods
|
||
|
|
intersect setops-methods
|
||
|
|
intersect,CompressedAtomicList,CompressedAtomicList-method AtomicList-utils
|
||
|
|
intersect,CompressedIRangesList,CompressedIRangesList-method setops-methods
|
||
|
|
intersect,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
intersect,IntegerRangesList,IntegerRangesList-method setops-methods
|
||
|
|
intersect,Pairs,missing-method setops-methods
|
||
|
|
intra-range-methods intra-range-methods
|
||
|
|
IPos IPos-class
|
||
|
|
IPos-class IPos-class
|
||
|
|
IPosRanges IPosRanges-class
|
||
|
|
IPosRanges-class IPosRanges-class
|
||
|
|
IPosRanges-comparison IPosRanges-comparison
|
||
|
|
IQR,AtomicList-method AtomicList-utils
|
||
|
|
IRanges IRanges-constructor
|
||
|
|
IRanges-class IRanges-class
|
||
|
|
IRanges-constructor IRanges-constructor
|
||
|
|
IRanges-utils IRanges-utils
|
||
|
|
IRangesList IRangesList-class
|
||
|
|
IRangesList-class IRangesList-class
|
||
|
|
is.na,CompressedList-method CompressedList-class
|
||
|
|
is.unsorted,IPosRanges-method IPosRanges-comparison
|
||
|
|
isDisjoint inter-range-methods
|
||
|
|
isDisjoint,IntegerRanges-method inter-range-methods
|
||
|
|
isDisjoint,IntegerRangesList-method inter-range-methods
|
||
|
|
isDisjoint,NormalIRanges-method inter-range-methods
|
||
|
|
isDisjoint,StitchedIPos-method inter-range-methods
|
||
|
|
isEmpty,NormalIRanges-method IRanges-class
|
||
|
|
isEmpty,Ranges-method IPosRanges-class
|
||
|
|
isNormal IPosRanges-class
|
||
|
|
isNormal,CompressedIRangesList-method IRangesList-class
|
||
|
|
isNormal,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
isNormal,IRanges-method IRanges-class
|
||
|
|
isNormal,NormalIRanges-method IRanges-class
|
||
|
|
isNormal,Ranges-method IPosRanges-class
|
||
|
|
isNormal,SimpleIRangesList-method IRangesList-class
|
||
|
|
lapply,CompressedAtomicList-method AtomicList-class
|
||
|
|
lapply,CompressedList-method CompressedList-class
|
||
|
|
length,CompressedList-method CompressedList-class
|
||
|
|
length,H2LGrouping-method Grouping-class
|
||
|
|
length,IPos-method IPos-class
|
||
|
|
length,MaskCollection-method MaskCollection-class
|
||
|
|
length,NCList-method NCList-class
|
||
|
|
length,NCLists-method NCList-class
|
||
|
|
length,PartitioningByEnd-method Grouping-class
|
||
|
|
length,PartitioningByWidth-method Grouping-class
|
||
|
|
length,Ranges-method IPosRanges-class
|
||
|
|
length,UnstitchedIPos-method IPos-class
|
||
|
|
length<-,H2LGrouping-method Grouping-class
|
||
|
|
LogicalList AtomicList-class
|
||
|
|
LogicalList-class AtomicList-class
|
||
|
|
low2high Grouping-class
|
||
|
|
low2high,H2LGrouping-method Grouping-class
|
||
|
|
mad,AtomicList-method AtomicList-utils
|
||
|
|
ManyToManyGrouping Grouping-class
|
||
|
|
ManyToManyGrouping-class Grouping-class
|
||
|
|
ManyToOneGrouping Grouping-class
|
||
|
|
ManyToOneGrouping-class Grouping-class
|
||
|
|
mapOrder Grouping-class
|
||
|
|
mapOrder,PartitioningMap-method Grouping-class
|
||
|
|
Mask MaskCollection-class
|
||
|
|
MaskCollection MaskCollection-class
|
||
|
|
MaskCollection-class MaskCollection-class
|
||
|
|
MaskCollection.show_frame MaskCollection-class
|
||
|
|
maskedratio MaskCollection-class
|
||
|
|
maskedratio,MaskCollection-method MaskCollection-class
|
||
|
|
maskedwidth MaskCollection-class
|
||
|
|
maskedwidth,MaskCollection-method MaskCollection-class
|
||
|
|
match,CompressedList,vector-method CompressedList-class
|
||
|
|
match,IPosRanges,IPosRanges-method IPosRanges-comparison
|
||
|
|
Math,AtomicList-method AtomicList-utils
|
||
|
|
Math,CompressedAtomicList-method AtomicList-utils
|
||
|
|
Math2,AtomicList-method AtomicList-utils
|
||
|
|
Math2,CompressedAtomicList-method AtomicList-utils
|
||
|
|
max,CompressedNormalIRangesList-method IRangesList-class
|
||
|
|
max,MaskCollection-method MaskCollection-class
|
||
|
|
max,NormalIRanges-method IRanges-class
|
||
|
|
max,SimpleNormalIRangesList-method IRangesList-class
|
||
|
|
max,Views-method view-summarization-methods
|
||
|
|
mean,AtomicList-method AtomicList-utils
|
||
|
|
mean,CompressedIntegerList-method AtomicList-utils
|
||
|
|
mean,CompressedLogicalList-method AtomicList-utils
|
||
|
|
mean,CompressedNumericList-method AtomicList-utils
|
||
|
|
mean,CompressedRleList-method AtomicList-utils
|
||
|
|
mean,Views-method view-summarization-methods
|
||
|
|
median,AtomicList-method AtomicList-utils
|
||
|
|
median,CompressedAtomicList-method AtomicList-utils
|
||
|
|
members Grouping-class
|
||
|
|
members,H2LGrouping-method Grouping-class
|
||
|
|
members,ManyToOneGrouping-method Grouping-class
|
||
|
|
merge,IntegerRangesList,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
merge,IntegerRangesList,missing-method IntegerRangesList-class
|
||
|
|
merge,missing,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
mergeByOverlaps findOverlaps-methods
|
||
|
|
mid IPosRanges-class
|
||
|
|
mid,Ranges-method IPosRanges-class
|
||
|
|
min,CompressedNormalIRangesList-method IRangesList-class
|
||
|
|
min,MaskCollection-method MaskCollection-class
|
||
|
|
min,NormalIRanges-method IRanges-class
|
||
|
|
min,SimpleNormalIRangesList-method IRangesList-class
|
||
|
|
min,Views-method view-summarization-methods
|
||
|
|
multisplit multisplit
|
||
|
|
names,CompressedList-method CompressedList-class
|
||
|
|
names,IPos-method IPos-class
|
||
|
|
names,IRanges-method IRanges-class
|
||
|
|
names,MaskCollection-method MaskCollection-class
|
||
|
|
names,NCList-method NCList-class
|
||
|
|
names,NCLists-method NCList-class
|
||
|
|
names,Partitioning-method Grouping-class
|
||
|
|
names,Views-method Views-class
|
||
|
|
names<-,CompressedList-method CompressedList-class
|
||
|
|
names<-,IPos-method IPos-class
|
||
|
|
names<-,IRanges-method IRanges-class
|
||
|
|
names<-,MaskCollection-method MaskCollection-class
|
||
|
|
names<-,Partitioning-method Grouping-class
|
||
|
|
names<-,Views-method Views-class
|
||
|
|
narrow intra-range-methods
|
||
|
|
narrow,ANY-method intra-range-methods
|
||
|
|
narrow,MaskCollection-method intra-range-methods
|
||
|
|
nchar,CompressedCharacterList-method AtomicList-utils
|
||
|
|
nchar,CompressedRleList-method AtomicList-utils
|
||
|
|
nchar,SimpleCharacterList-method AtomicList-utils
|
||
|
|
nchar,SimpleRleList-method AtomicList-utils
|
||
|
|
NCList NCList-class
|
||
|
|
NCList-class NCList-class
|
||
|
|
NCLists NCList-class
|
||
|
|
NCLists-class NCList-class
|
||
|
|
ncol,CompressedSplitDataFrameList-method DataFrameList-class
|
||
|
|
ncol,DataFrameList-method DataFrameList-class
|
||
|
|
ncol,SimpleSplitDataFrameList-method DataFrameList-class
|
||
|
|
ncols,CompressedSplitDataFrameList-method DataFrameList-class
|
||
|
|
ncols,DataFrameList-method DataFrameList-class
|
||
|
|
ncols,SimpleSplitDataFrameList-method DataFrameList-class
|
||
|
|
nearest nearest-methods
|
||
|
|
nearest,IntegerRanges,IntegerRanges_OR_missing-method nearest-methods
|
||
|
|
nearest-methods nearest-methods
|
||
|
|
nir_list MaskCollection-class
|
||
|
|
nir_list,MaskCollection-method MaskCollection-class
|
||
|
|
nLnode,CompressedHitsList-method CompressedHitsList-class
|
||
|
|
nobj Grouping-class
|
||
|
|
nobj,BaseManyToManyGrouping-method Grouping-class
|
||
|
|
nobj,CompressedManyToOneGrouping-method Grouping-class
|
||
|
|
nobj,H2LGrouping-method Grouping-class
|
||
|
|
nobj,ManyToManyGrouping-method Grouping-class
|
||
|
|
nobj,ManyToOneGrouping-method Grouping-class
|
||
|
|
nobj,PartitioningByEnd-method Grouping-class
|
||
|
|
NormalIRanges IRanges-class
|
||
|
|
NormalIRanges-class IRanges-class
|
||
|
|
NormalIRangesList IRangesList-class
|
||
|
|
NormalIRangesList-class IRangesList-class
|
||
|
|
nRnode,CompressedHitsList-method CompressedHitsList-class
|
||
|
|
NROW,DataFrameList-method DataFrameList-class
|
||
|
|
nrow,DataFrameList-method DataFrameList-class
|
||
|
|
nrows,DataFrameList-method DataFrameList-class
|
||
|
|
NumericList AtomicList-class
|
||
|
|
NumericList-class AtomicList-class
|
||
|
|
Ops,atomic,AtomicList-method AtomicList-utils
|
||
|
|
Ops,atomic,CompressedAtomicList-method AtomicList-utils
|
||
|
|
Ops,AtomicList,atomic-method AtomicList-utils
|
||
|
|
Ops,AtomicList,AtomicList-method AtomicList-utils
|
||
|
|
Ops,AtomicList,missing-method AtomicList-utils
|
||
|
|
Ops,CompressedAtomicList,atomic-method AtomicList-utils
|
||
|
|
Ops,CompressedAtomicList,CompressedAtomicList-method AtomicList-utils
|
||
|
|
Ops,CompressedAtomicList,SimpleAtomicList-method AtomicList-utils
|
||
|
|
Ops,CompressedRangesList,numeric-method intra-range-methods
|
||
|
|
Ops,Ranges,numeric-method intra-range-methods
|
||
|
|
Ops,RangesList,numeric-method intra-range-methods
|
||
|
|
Ops,SimpleAtomicList,CompressedAtomicList-method AtomicList-utils
|
||
|
|
order,CompressedAtomicList-method AtomicList-utils
|
||
|
|
order,IPosRanges-method IPosRanges-comparison
|
||
|
|
order,List-method AtomicList-class
|
||
|
|
overlapsAny findOverlaps-methods
|
||
|
|
overlapsAny,integer,Vector-method findOverlaps-methods
|
||
|
|
overlapsAny,IntegerRangesList,IntegerRangesList-method findOverlaps-methods
|
||
|
|
overlapsAny,Vector,missing-method findOverlaps-methods
|
||
|
|
overlapsAny,Vector,Vector-method findOverlaps-methods
|
||
|
|
overlapsRanges findOverlaps-methods
|
||
|
|
overlapsRanges,IntegerRanges,IntegerRanges-method findOverlaps-methods
|
||
|
|
overlapsRanges,IntegerRangesList,IntegerRangesList-method findOverlaps-methods
|
||
|
|
parallel_slot_names,IPos-method IPos-class
|
||
|
|
parallel_slot_names,IRanges-method IRanges-class
|
||
|
|
parallel_slot_names,NCLists-method NCList-class
|
||
|
|
parallel_slot_names,Partitioning-method Grouping-class
|
||
|
|
parallel_slot_names,PartitioningByEnd-method Grouping-class
|
||
|
|
parallel_slot_names,PartitioningByWidth-method Grouping-class
|
||
|
|
parallel_slot_names,UnstitchedIPos-method IPos-class
|
||
|
|
parallel_slot_names,Views-method Views-class
|
||
|
|
Partitioning Grouping-class
|
||
|
|
Partitioning-class Grouping-class
|
||
|
|
PartitioningByEnd Grouping-class
|
||
|
|
PartitioningByEnd-class Grouping-class
|
||
|
|
PartitioningByWidth Grouping-class
|
||
|
|
PartitioningByWidth-class Grouping-class
|
||
|
|
PartitioningMap Grouping-class
|
||
|
|
PartitioningMap-class Grouping-class
|
||
|
|
paste,CompressedAtomicList-method AtomicList-utils
|
||
|
|
pcompare IPosRanges-comparison
|
||
|
|
pcompare,IPosRanges,IPosRanges-method IPosRanges-comparison
|
||
|
|
pgap setops-methods
|
||
|
|
pgap,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
pintersect setops-methods
|
||
|
|
pintersect,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
pintersect,Pairs,missing-method setops-methods
|
||
|
|
pmax,IntegerList-method AtomicList-utils
|
||
|
|
pmax,NumericList-method AtomicList-utils
|
||
|
|
pmax,RleList-method AtomicList-utils
|
||
|
|
pmax.int,IntegerList-method AtomicList-utils
|
||
|
|
pmax.int,NumericList-method AtomicList-utils
|
||
|
|
pmax.int,RleList-method AtomicList-utils
|
||
|
|
pmin,IntegerList-method AtomicList-utils
|
||
|
|
pmin,NumericList-method AtomicList-utils
|
||
|
|
pmin,RleList-method AtomicList-utils
|
||
|
|
pmin.int,IntegerList-method AtomicList-utils
|
||
|
|
pmin.int,NumericList-method AtomicList-utils
|
||
|
|
pmin.int,RleList-method AtomicList-utils
|
||
|
|
pos IPos-class
|
||
|
|
pos,CompressedPosList-method IRangesList-class
|
||
|
|
pos,IPos-method IPos-class
|
||
|
|
pos,PosList-method IntegerRangesList-class
|
||
|
|
pos,UnstitchedIPos-method IPos-class
|
||
|
|
poverlaps findOverlaps-methods
|
||
|
|
poverlaps,integer,IntegerRanges-method findOverlaps-methods
|
||
|
|
poverlaps,IntegerRanges,integer-method findOverlaps-methods
|
||
|
|
poverlaps,IntegerRanges,IntegerRanges-method findOverlaps-methods
|
||
|
|
precede nearest-methods
|
||
|
|
precede,IntegerRanges,IntegerRanges_OR_missing-method nearest-methods
|
||
|
|
promoters intra-range-methods
|
||
|
|
promoters,IntegerRanges-method intra-range-methods
|
||
|
|
promoters,RangesList-method intra-range-methods
|
||
|
|
psetdiff setops-methods
|
||
|
|
psetdiff,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
psetdiff,Pairs,missing-method setops-methods
|
||
|
|
punion setops-methods
|
||
|
|
punion,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
punion,Pairs,missing-method setops-methods
|
||
|
|
quantile,AtomicList-method AtomicList-utils
|
||
|
|
range inter-range-methods
|
||
|
|
range,CompressedIntegerList-method AtomicList-utils
|
||
|
|
range,CompressedIRangesList-method inter-range-methods
|
||
|
|
range,CompressedLogicalList-method AtomicList-utils
|
||
|
|
range,CompressedNumericList-method AtomicList-utils
|
||
|
|
range,IntegerRanges-method inter-range-methods
|
||
|
|
range,IntegerRangesList-method inter-range-methods
|
||
|
|
range,StitchedIPos-method inter-range-methods
|
||
|
|
range-squeezers range-squeezers
|
||
|
|
rangeComparisonCodeToLetter IPosRanges-comparison
|
||
|
|
RangedSelection RangedSelection-class
|
||
|
|
RangedSelection-class RangedSelection-class
|
||
|
|
ranges range-squeezers
|
||
|
|
ranges,CompressedRleList-method AtomicList-class
|
||
|
|
ranges,IntegerRanges-method IRanges-class
|
||
|
|
ranges,NCLists-method NCList-class
|
||
|
|
ranges,RangedSelection-method RangedSelection-class
|
||
|
|
ranges,Rle-method Rle-class-leftovers
|
||
|
|
ranges,RleList-method AtomicList-class
|
||
|
|
ranges,SimpleViewsList-method ViewsList-class
|
||
|
|
ranges,Views-method Views-class
|
||
|
|
ranges<- Views-class
|
||
|
|
ranges<-,RangedSelection-method RangedSelection-class
|
||
|
|
ranges<-,Views-method Views-class
|
||
|
|
rank,CompressedAtomicList-method AtomicList-utils
|
||
|
|
rank,List-method AtomicList-class
|
||
|
|
RawList AtomicList-class
|
||
|
|
RawList-class AtomicList-class
|
||
|
|
rbind,DataFrameList-method DataFrameList-class
|
||
|
|
read.agpMask read.Mask
|
||
|
|
read.gapMask read.Mask
|
||
|
|
read.liftMask read.Mask
|
||
|
|
read.Mask read.Mask
|
||
|
|
read.rmMask read.Mask
|
||
|
|
read.trfMask read.Mask
|
||
|
|
reduce inter-range-methods
|
||
|
|
reduce,CompressedIRangesList-method inter-range-methods
|
||
|
|
reduce,IntegerRanges-method inter-range-methods
|
||
|
|
reduce,IntegerRangesList-method inter-range-methods
|
||
|
|
reduce,Views-method inter-range-methods
|
||
|
|
reflect intra-range-methods
|
||
|
|
reflect,IntegerRanges-method intra-range-methods
|
||
|
|
regroup extractList
|
||
|
|
relist extractList
|
||
|
|
relist,ANY,List-method extractList
|
||
|
|
relist,ANY,PartitioningByEnd-method extractList
|
||
|
|
relist,Vector,list-method extractList
|
||
|
|
resize intra-range-methods
|
||
|
|
resize,Ranges-method intra-range-methods
|
||
|
|
resize,RangesList-method intra-range-methods
|
||
|
|
restrict intra-range-methods
|
||
|
|
restrict,IntegerRanges-method intra-range-methods
|
||
|
|
restrict,RangesList-method intra-range-methods
|
||
|
|
restrict,Views-method intra-range-methods
|
||
|
|
revElements,CompressedList-method CompressedList-class
|
||
|
|
reverse reverse-methods
|
||
|
|
reverse,character-method reverse-methods
|
||
|
|
reverse,IRanges-method reverse-methods
|
||
|
|
reverse,MaskCollection-method reverse-methods
|
||
|
|
reverse,NormalIRanges-method reverse-methods
|
||
|
|
reverse,Views-method reverse-methods
|
||
|
|
rglist range-squeezers
|
||
|
|
rglist,Pairs-method range-squeezers
|
||
|
|
RleList AtomicList-class
|
||
|
|
RleList,AtomicList,RleList-method AtomicList-class
|
||
|
|
RleList-class AtomicList-class
|
||
|
|
RleViews RleViews-class
|
||
|
|
RleViews-class RleViews-class
|
||
|
|
RleViewsList RleViewsList-class
|
||
|
|
RleViewsList-class RleViewsList-class
|
||
|
|
ROWNAMES,DataFrameList-method DataFrameList-class
|
||
|
|
rownames,DataFrameList-method DataFrameList-class
|
||
|
|
rownames<-,CompressedSplitDataFrameList-method DataFrameList-class
|
||
|
|
ROWNAMES<-,DataFrameList-method DataFrameList-class
|
||
|
|
rownames<-,SimpleDataFrameList-method DataFrameList-class
|
||
|
|
runLength,CompressedRleList-method AtomicList-class
|
||
|
|
runLength,RleList-method AtomicList-class
|
||
|
|
runmean,RleList-method AtomicList-utils
|
||
|
|
runmed,CompressedIntegerList-method AtomicList-utils
|
||
|
|
runmed,NumericList-method AtomicList-utils
|
||
|
|
runmed,RleList-method AtomicList-utils
|
||
|
|
runmed,SimpleIntegerList-method AtomicList-utils
|
||
|
|
runq,RleList-method AtomicList-utils
|
||
|
|
runsum,RleList-method AtomicList-utils
|
||
|
|
runValue,CompressedRleList-method AtomicList-class
|
||
|
|
runValue,RleList-method AtomicList-class
|
||
|
|
runValue<-,CompressedRleList-method AtomicList-class
|
||
|
|
runValue<-,SimpleRleList-method AtomicList-class
|
||
|
|
runwtsum,RleList-method AtomicList-utils
|
||
|
|
sd,AtomicList-method AtomicList-utils
|
||
|
|
selectNearest nearest-methods
|
||
|
|
selfmatch,CompressedAtomicList-method AtomicList-utils
|
||
|
|
selfmatch,IPosRanges-method IPosRanges-comparison
|
||
|
|
setdiff setops-methods
|
||
|
|
setdiff,CompressedIRangesList,CompressedIRangesList-method setops-methods
|
||
|
|
setdiff,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
setdiff,IntegerRangesList,IntegerRangesList-method setops-methods
|
||
|
|
setdiff,Pairs,missing-method setops-methods
|
||
|
|
setops-methods setops-methods
|
||
|
|
shift intra-range-methods
|
||
|
|
shift,IPos-method intra-range-methods
|
||
|
|
shift,Ranges-method intra-range-methods
|
||
|
|
shift,RangesList-method intra-range-methods
|
||
|
|
show,AtomicList-method AtomicList-class
|
||
|
|
show,Dups-method Grouping-class
|
||
|
|
show,Grouping-method Grouping-class
|
||
|
|
show,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
show,IPos-method IPos-class
|
||
|
|
show,IPosRanges-method IPosRanges-class
|
||
|
|
show,MaskCollection-method MaskCollection-class
|
||
|
|
show,PartitioningMap-method Grouping-class
|
||
|
|
show,RleList-method AtomicList-class
|
||
|
|
show,RleViews-method RleViews-class
|
||
|
|
show,SplitDataFrameList-method DataFrameList-class
|
||
|
|
SimpleAtomicList AtomicList-class
|
||
|
|
SimpleAtomicList-class AtomicList-class
|
||
|
|
SimpleCharacterList AtomicList-class
|
||
|
|
SimpleCharacterList-class AtomicList-class
|
||
|
|
SimpleComplexList AtomicList-class
|
||
|
|
SimpleComplexList-class AtomicList-class
|
||
|
|
SimpleDataFrameList DataFrameList-class
|
||
|
|
SimpleDataFrameList-class DataFrameList-class
|
||
|
|
SimpleDFrameList DataFrameList-class
|
||
|
|
SimpleDFrameList-class DataFrameList-class
|
||
|
|
SimpleFactorList AtomicList-class
|
||
|
|
SimpleFactorList-class AtomicList-class
|
||
|
|
SimpleGrouping-class Grouping-class
|
||
|
|
SimpleIntegerList AtomicList-class
|
||
|
|
SimpleIntegerList-class AtomicList-class
|
||
|
|
SimpleIntegerRangesList IntegerRangesList-class
|
||
|
|
SimpleIntegerRangesList-class IntegerRangesList-class
|
||
|
|
SimpleIRangesList IRangesList-class
|
||
|
|
SimpleIRangesList-class IRangesList-class
|
||
|
|
SimpleLogicalList AtomicList-class
|
||
|
|
SimpleLogicalList-class AtomicList-class
|
||
|
|
SimpleManyToManyGrouping-class Grouping-class
|
||
|
|
SimpleManyToOneGrouping-class Grouping-class
|
||
|
|
SimpleNormalIRangesList IRangesList-class
|
||
|
|
SimpleNormalIRangesList-class IRangesList-class
|
||
|
|
SimpleNumericList AtomicList-class
|
||
|
|
SimpleNumericList-class AtomicList-class
|
||
|
|
SimpleRawList AtomicList-class
|
||
|
|
SimpleRawList-class AtomicList-class
|
||
|
|
SimpleRleList AtomicList-class
|
||
|
|
SimpleRleList-class AtomicList-class
|
||
|
|
SimpleRleViewsList-class RleViewsList-class
|
||
|
|
SimpleSplitDataFrameList DataFrameList-class
|
||
|
|
SimpleSplitDataFrameList-class DataFrameList-class
|
||
|
|
SimpleSplitDFrameList DataFrameList-class
|
||
|
|
SimpleSplitDFrameList-class DataFrameList-class
|
||
|
|
SimpleViewsList ViewsList-class
|
||
|
|
SimpleViewsList-class ViewsList-class
|
||
|
|
slice slice-methods
|
||
|
|
slice,ANY-method slice-methods
|
||
|
|
slice,Rle-method slice-methods
|
||
|
|
slice,RleList-method slice-methods
|
||
|
|
slice-methods slice-methods
|
||
|
|
slidingWindows IPosRanges-class
|
||
|
|
slidingWindows,IPosRanges-method IPosRanges-class
|
||
|
|
smoothEnds,CompressedIntegerList-method AtomicList-utils
|
||
|
|
smoothEnds,NumericList-method AtomicList-utils
|
||
|
|
smoothEnds,RleList-method AtomicList-utils
|
||
|
|
smoothEnds,SimpleIntegerList-method AtomicList-utils
|
||
|
|
solveUserSEW IRanges-constructor
|
||
|
|
sort,List-method AtomicList-class
|
||
|
|
space IntegerRangesList-class
|
||
|
|
space,CompressedHitsList-method CompressedHitsList-class
|
||
|
|
space,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
split<-,Vector-method seqapply
|
||
|
|
SplitDataFrameList DataFrameList-class
|
||
|
|
SplitDataFrameList-class DataFrameList-class
|
||
|
|
SplitDFrameList DataFrameList-class
|
||
|
|
SplitDFrameList-class DataFrameList-class
|
||
|
|
splitRanges Rle-class-leftovers
|
||
|
|
splitRanges,Rle-method Rle-class-leftovers
|
||
|
|
splitRanges,vector_OR_factor-method Rle-class-leftovers
|
||
|
|
stack,DataFrameList-method DataFrameList-class
|
||
|
|
start,CompressedRangesList-method IRangesList-class
|
||
|
|
start,IRanges-method IRanges-class
|
||
|
|
start,NCList-method NCList-class
|
||
|
|
start,NCLists-method NCList-class
|
||
|
|
start,PartitioningByEnd-method Grouping-class
|
||
|
|
start,PartitioningByWidth-method Grouping-class
|
||
|
|
start,Pos-method IPosRanges-class
|
||
|
|
start,Ranges-method IPosRanges-class
|
||
|
|
start,RangesList-method IntegerRangesList-class
|
||
|
|
start,SimpleViewsList-method ViewsList-class
|
||
|
|
start,Views-method Views-class
|
||
|
|
start<- IPosRanges-class
|
||
|
|
start<-,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
start<-,IRanges-method IRanges-class
|
||
|
|
start<-,Views-method Views-class
|
||
|
|
startsWith,CharacterList,ANY-method AtomicList-utils
|
||
|
|
startsWith,RleList,ANY-method AtomicList-utils
|
||
|
|
StitchedIPos IPos-class
|
||
|
|
StitchedIPos-class IPos-class
|
||
|
|
sub,ANY,ANY,CompressedCharacterList-method AtomicList-utils
|
||
|
|
sub,ANY,ANY,CompressedRleList-method AtomicList-utils
|
||
|
|
sub,ANY,ANY,SimpleCharacterList-method AtomicList-utils
|
||
|
|
sub,ANY,ANY,SimpleRleList-method AtomicList-utils
|
||
|
|
subject Views-class
|
||
|
|
subject,SimpleRleViewsList-method RleViewsList-class
|
||
|
|
subject,Views-method Views-class
|
||
|
|
subsetByOverlaps findOverlaps-methods
|
||
|
|
subsetByOverlaps,Vector,Vector-method findOverlaps-methods
|
||
|
|
subviews Views-class
|
||
|
|
subviews,Views-method Views-class
|
||
|
|
successiveIRanges IRanges-utils
|
||
|
|
successiveViews Views-class
|
||
|
|
sum,CompressedIntegerList-method AtomicList-utils
|
||
|
|
sum,CompressedLogicalList-method AtomicList-utils
|
||
|
|
sum,CompressedNumericList-method AtomicList-utils
|
||
|
|
sum,Views-method view-summarization-methods
|
||
|
|
Summary,AtomicList-method AtomicList-utils
|
||
|
|
summary,CompressedIRangesList-method IRangesList-class
|
||
|
|
Summary,CompressedRleList-method AtomicList-utils
|
||
|
|
summary,IPos-method IPos-class
|
||
|
|
summary,IPosRanges-method IPosRanges-class
|
||
|
|
Summary,Views-method view-summarization-methods
|
||
|
|
summary.IPos IPos-class
|
||
|
|
summary.IPosRanges IPosRanges-class
|
||
|
|
table,AtomicList-method AtomicList-class
|
||
|
|
table,SimpleAtomicList-method AtomicList-class
|
||
|
|
tapply,ANY,Vector-method Vector-class-leftovers
|
||
|
|
tapply,Vector,ANY-method Vector-class-leftovers
|
||
|
|
tapply,Vector,Vector-method Vector-class-leftovers
|
||
|
|
terminators intra-range-methods
|
||
|
|
terminators,IntegerRanges-method intra-range-methods
|
||
|
|
terminators,RangesList-method intra-range-methods
|
||
|
|
threebands intra-range-methods
|
||
|
|
threebands,IRanges-method intra-range-methods
|
||
|
|
tile IPosRanges-class
|
||
|
|
tile,IPosRanges-method IPosRanges-class
|
||
|
|
to,CompressedHitsList-method CompressedHitsList-class
|
||
|
|
togroup Grouping-class
|
||
|
|
togroup,ANY-method Grouping-class
|
||
|
|
togroup,H2LGrouping-method Grouping-class
|
||
|
|
togroup,ManyToOneGrouping-method Grouping-class
|
||
|
|
togroup,Partitioning-method Grouping-class
|
||
|
|
togrouplength Grouping-class
|
||
|
|
togrouplength,ManyToOneGrouping-method Grouping-class
|
||
|
|
togrouprank Grouping-class
|
||
|
|
togrouprank,H2LGrouping-method Grouping-class
|
||
|
|
tolower,CompressedCharacterList-method AtomicList-utils
|
||
|
|
tolower,CompressedRleList-method AtomicList-utils
|
||
|
|
tolower,SimpleCharacterList-method AtomicList-utils
|
||
|
|
tolower,SimpleRleList-method AtomicList-utils
|
||
|
|
toupper,CompressedCharacterList-method AtomicList-utils
|
||
|
|
toupper,CompressedRleList-method AtomicList-utils
|
||
|
|
toupper,SimpleCharacterList-method AtomicList-utils
|
||
|
|
toupper,SimpleRleList-method AtomicList-utils
|
||
|
|
transform,SplitDataFrameList-method DataFrameList-class
|
||
|
|
trim Views-class
|
||
|
|
trim,Views-method Views-class
|
||
|
|
union setops-methods
|
||
|
|
union,CompressedIRangesList,CompressedIRangesList-method setops-methods
|
||
|
|
union,IntegerRanges,IntegerRanges-method setops-methods
|
||
|
|
union,IntegerRangesList,IntegerRangesList-method setops-methods
|
||
|
|
union,Pairs,missing-method setops-methods
|
||
|
|
unique,CompressedList-method AtomicList-class
|
||
|
|
unique,RleList-method AtomicList-class
|
||
|
|
unlist,CompressedList-method CompressedList-class
|
||
|
|
unlist,SimpleFactorList-method AtomicList-class
|
||
|
|
unlist,SimpleNormalIRangesList-method IRangesList-class
|
||
|
|
unlist,SimpleRleList-method AtomicList-class
|
||
|
|
unlist,Views-method Views-class
|
||
|
|
unsplit,List-method seqapply
|
||
|
|
UnstitchedIPos IPos-class
|
||
|
|
UnstitchedIPos-class IPos-class
|
||
|
|
unstrsplit,CharacterList-method AtomicList-utils
|
||
|
|
unstrsplit,RleList-method AtomicList-utils
|
||
|
|
updateObject,IPos-method IPos-class
|
||
|
|
update_ranges intra-range-methods
|
||
|
|
update_ranges,IRanges-method intra-range-methods
|
||
|
|
update_ranges,Views-method intra-range-methods
|
||
|
|
var,AtomicList,AtomicList-method AtomicList-utils
|
||
|
|
var,AtomicList,missing-method AtomicList-utils
|
||
|
|
view-summarization-methods view-summarization-methods
|
||
|
|
viewApply view-summarization-methods
|
||
|
|
viewApply,RleViews-method view-summarization-methods
|
||
|
|
viewApply,RleViewsList-method view-summarization-methods
|
||
|
|
viewApply,Views-method view-summarization-methods
|
||
|
|
viewMaxs view-summarization-methods
|
||
|
|
viewMaxs,RleViews-method view-summarization-methods
|
||
|
|
viewMaxs,RleViewsList-method view-summarization-methods
|
||
|
|
viewMeans view-summarization-methods
|
||
|
|
viewMeans,RleViews-method view-summarization-methods
|
||
|
|
viewMeans,RleViewsList-method view-summarization-methods
|
||
|
|
viewMins view-summarization-methods
|
||
|
|
viewMins,RleViews-method view-summarization-methods
|
||
|
|
viewMins,RleViewsList-method view-summarization-methods
|
||
|
|
viewRangeMaxs view-summarization-methods
|
||
|
|
viewRangeMaxs,RleViews-method view-summarization-methods
|
||
|
|
viewRangeMaxs,RleViewsList-method view-summarization-methods
|
||
|
|
viewRangeMins view-summarization-methods
|
||
|
|
viewRangeMins,RleViews-method view-summarization-methods
|
||
|
|
viewRangeMins,RleViewsList-method view-summarization-methods
|
||
|
|
Views Views-class
|
||
|
|
Views,Rle-method RleViews-class
|
||
|
|
Views,RleList-method RleViewsList-class
|
||
|
|
Views-class Views-class
|
||
|
|
ViewsList ViewsList-class
|
||
|
|
ViewsList-class ViewsList-class
|
||
|
|
viewSums view-summarization-methods
|
||
|
|
viewSums,RleViews-method view-summarization-methods
|
||
|
|
viewSums,RleViewsList-method view-summarization-methods
|
||
|
|
viewWhichMaxs view-summarization-methods
|
||
|
|
viewWhichMaxs,RleViews-method view-summarization-methods
|
||
|
|
viewWhichMaxs,RleViewsList-method view-summarization-methods
|
||
|
|
viewWhichMins view-summarization-methods
|
||
|
|
viewWhichMins,RleViews-method view-summarization-methods
|
||
|
|
viewWhichMins,RleViewsList-method view-summarization-methods
|
||
|
|
vmembers Grouping-class
|
||
|
|
vmembers,H2LGrouping-method Grouping-class
|
||
|
|
vmembers,ManyToOneGrouping-method Grouping-class
|
||
|
|
which,CompressedLogicalList-method AtomicList-utils
|
||
|
|
which,CompressedRleList-method AtomicList-utils
|
||
|
|
which,SimpleLogicalList-method AtomicList-utils
|
||
|
|
which,SimpleRleList-method AtomicList-utils
|
||
|
|
which.max,CompressedRleList-method AtomicList-utils
|
||
|
|
which.max,IntegerList-method AtomicList-utils
|
||
|
|
which.max,NumericList-method AtomicList-utils
|
||
|
|
which.max,RleList-method AtomicList-utils
|
||
|
|
which.max,Views-method view-summarization-methods
|
||
|
|
which.min,CompressedRleList-method AtomicList-utils
|
||
|
|
which.min,IntegerList-method AtomicList-utils
|
||
|
|
which.min,NumericList-method AtomicList-utils
|
||
|
|
which.min,RleList-method AtomicList-utils
|
||
|
|
which.min,Views-method view-summarization-methods
|
||
|
|
whichAsIRanges IRanges-utils
|
||
|
|
whichFirstNotNormal IPosRanges-class
|
||
|
|
whichFirstNotNormal,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
whichFirstNotNormal,Ranges-method IPosRanges-class
|
||
|
|
width IPosRanges-class
|
||
|
|
width,CompressedRangesList-method IRangesList-class
|
||
|
|
width,IRanges-method IRanges-class
|
||
|
|
width,MaskCollection-method MaskCollection-class
|
||
|
|
width,NCList-method NCList-class
|
||
|
|
width,NCLists-method NCList-class
|
||
|
|
width,PartitioningByEnd-method Grouping-class
|
||
|
|
width,PartitioningByWidth-method Grouping-class
|
||
|
|
width,Pos-method IPosRanges-class
|
||
|
|
width,Ranges-method IPosRanges-class
|
||
|
|
width,RangesList-method IntegerRangesList-class
|
||
|
|
width,SimpleViewsList-method ViewsList-class
|
||
|
|
width,Views-method Views-class
|
||
|
|
width<- IPosRanges-class
|
||
|
|
width<-,IntegerRangesList-method IntegerRangesList-class
|
||
|
|
width<-,IRanges-method IRanges-class
|
||
|
|
width<-,Views-method Views-class
|
||
|
|
window<-,factor-method Vector-class-leftovers
|
||
|
|
window<-,Vector-method Vector-class-leftovers
|
||
|
|
window<-,vector-method Vector-class-leftovers
|
||
|
|
window<-.factor Vector-class-leftovers
|
||
|
|
window<-.Vector Vector-class-leftovers
|
||
|
|
window<-.vector Vector-class-leftovers
|
||
|
|
windows,Ranges-method intra-range-methods
|
||
|
|
with,Vector-method Vector-class-leftovers
|
||
|
|
[,CompressedSplitDataFrameList-method DataFrameList-class
|
||
|
|
[,SimpleSplitDataFrameList-method DataFrameList-class
|
||
|
|
[<-,SplitDataFrameList-method DataFrameList-class
|
||
|
|
[[,SDFLWrapperForTransform-method DataFrameList-class
|
||
|
|
[[<-,SDFLWrapperForTransform-method DataFrameList-class
|