900 lines
31 KiB
Plaintext
900 lines
31 KiB
Plaintext
!,Rle-method Rle-utils
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!=,ANY,Vector-method Vector-comparison
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!=,Vector,ANY-method Vector-comparison
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!=,Vector,Vector-method Vector-comparison
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$,DataFrameFactor-method DataFrameFactor-class
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$,List-method List-class
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$<-,List-method List-class
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%in%,ANY,Vector-method Vector-comparison
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%in%,Rle,ANY-method Rle-class
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%in%,Vector,ANY-method Vector-comparison
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%in%,Vector,Vector-method Vector-comparison
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&,FilterRules,FilterRules-method FilterRules-class
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.Call2 S4Vectors-internals
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<,ANY,Vector-method Vector-comparison
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<,Vector,ANY-method Vector-comparison
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<,Vector,Vector-method Vector-comparison
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<=,ANY,Vector-method Vector-comparison
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<=,DataFrame,DataFrame-method DataFrame-comparison
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<=,Vector,ANY-method Vector-comparison
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<=,Vector,Vector-method Vector-comparison
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==,ANY,Vector-method Vector-comparison
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==,DataFrame,DataFrame-method DataFrame-comparison
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==,Vector,ANY-method Vector-comparison
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==,Vector,Vector-method Vector-comparison
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>,ANY,Vector-method Vector-comparison
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>,Vector,ANY-method Vector-comparison
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>,Vector,Vector-method Vector-comparison
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>=,ANY,Vector-method Vector-comparison
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>=,Vector,ANY-method Vector-comparison
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>=,Vector,Vector-method Vector-comparison
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active FilterRules-class
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active,FilterRules-method FilterRules-class
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active<- FilterRules-class
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active<-,FilterRules-method FilterRules-class
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aggregate aggregate-methods
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aggregate,data.frame-method aggregate-methods
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aggregate,List-method aggregate-methods
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aggregate,matrix-method aggregate-methods
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aggregate,Rle-method aggregate-methods
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aggregate,ts-method aggregate-methods
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aggregate,Vector-method aggregate-methods
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aggregate-methods aggregate-methods
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aggregate.Vector aggregate-methods
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Annotated Annotated-class
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Annotated-class Annotated-class
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anyDuplicated,NSBS-method subsetting-utils
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anyDuplicated,RangeNSBS-method subsetting-utils
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anyDuplicated,Rle-method Rle-class
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anyDuplicated,RleNSBS-method Rle-class
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anyDuplicated,Vector-method Vector-comparison
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anyDuplicated.NSBS subsetting-utils
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anyDuplicated.Rle Rle-class
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anyDuplicated.Vector Vector-comparison
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anyNA,Rle-method Rle-class
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anyNA,Vector-method Vector-class
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append Vector-class
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append,Rle,vector-method Rle-class
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append,vector,Rle-method Rle-class
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append,Vector,Vector-method Vector-class
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as.character,Factor-method Factor-class
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as.character,LLint-method LLint-class
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as.character,Vector-method Vector-class
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as.character.LLint LLint-class
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as.complex,Vector-method Vector-class
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as.data.frame,DataFrame-method DataFrame-class
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as.data.frame,Hits-method Hits-class
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as.data.frame,List-method List-class
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as.data.frame,Pairs-method Pairs-class
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as.data.frame,Rle-method Rle-class
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as.data.frame,Vector-method Vector-class
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as.data.frame.DataFrame DataFrame-class
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as.data.frame.Hits Hits-class
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as.data.frame.Vector Vector-class
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as.double,Vector-method Vector-class
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as.env Vector-class
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as.env,NULL-method Vector-class
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as.env,SimpleList-method SimpleList-class
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as.env,Vector-method Vector-class
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as.factor,Factor-method Factor-class
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as.factor,Rle-method Rle-class
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as.integer,Factor-method Factor-class
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as.integer,LLint-method LLint-class
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as.integer,NativeNSBS-method subsetting-utils
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as.integer,RangeNSBS-method subsetting-utils
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as.integer,RleNSBS-method Rle-class
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as.integer,Vector-method Vector-class
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as.integer.LLint LLint-class
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as.list,List-method List-class
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as.list,Rle-method Rle-class
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as.list,SimpleList-method SimpleList-class
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as.list,TransposedDataFrame-method TransposedDataFrame-class
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as.list,Vector-method Vector-class
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as.list.Rle Rle-class
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as.list.SimpleList SimpleList-class
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as.list.TransposedDataFrame TransposedDataFrame-class
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as.list.Vector Vector-class
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as.LLint LLint-class
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as.logical,LLint-method LLint-class
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as.logical,Vector-method Vector-class
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as.logical.LLint LLint-class
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as.matrix,DataFrame-method DataFrame-class
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as.matrix,Hits-method Hits-class
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as.matrix,HitsList-method HitsList-class
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as.matrix,TransposedDataFrame-method TransposedDataFrame-class
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as.matrix,Vector-method Vector-class
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as.matrix.Vector Vector-class
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as.numeric,LLint-method LLint-class
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as.numeric,Vector-method Vector-class
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as.numeric.LLint LLint-class
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as.raw,Factor-method Factor-class
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as.raw,Vector-method Vector-class
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as.table,Hits-method Hits-class
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as.table,HitsList-method HitsList-class
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as.vector,Rle-method Rle-class
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as.vector.Rle Rle-class
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atomic S4Vectors-internals
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atomic-class S4Vectors-internals
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bindCOLS bindROWS
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bindCOLS,TransposedDataFrame-method TransposedDataFrame-class
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bindROWS bindROWS
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bindROWS,ANY-method bindROWS
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bindROWS,DataFrame-method DataFrame-combine
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bindROWS,Factor-method Factor-class
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bindROWS,Hits-method Hits-class
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bindROWS,LLint-method LLint-class
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bindROWS,NULL-method bindROWS
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bindROWS,Rle-method Rle-class
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bindROWS,TransposedDataFrame-method TransposedDataFrame-class
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bindROWS,Vector-method Vector-class
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breakTies Hits-class
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c Vector-class
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c,DataFrame-method DataFrame-combine
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c,LLint-method LLint-class
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c,Vector-method Vector-class
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cbind,DataFrame-method DataFrame-combine
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cbind,FilterMatrix-method FilterMatrix-class
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cbind,List-method List-utils
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cbind,RectangularData-method RectangularData-class
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cbind.DataFrame DataFrame-combine
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cbind.List List-utils
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cbind.RectangularData RectangularData-class
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cbind_mcols_for_display show-utils
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character_OR_NULL S4Vectors-internals
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character_OR_NULL-class S4Vectors-internals
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chartr,ANY,ANY,Rle-method Rle-utils
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class:atomic S4Vectors-internals
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class:character_OR_NULL S4Vectors-internals
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class:DataFrame DataFrame-class
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class:DataFrameFactor DataFrameFactor-class
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class:DataFrame_OR_NULL S4Vectors-internals
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class:DFrame DataFrame-class
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class:expression_OR_function FilterRules-class
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class:Factor Factor-class
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class:FilterRules FilterRules-class
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class:Hits Hits-class
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class:HitsList HitsList-class
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class:integer_OR_LLint LLint-class
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class:integer_OR_raw Factor-class
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class:List List-class
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class:list_OR_List List-class
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class:LLint LLint-class
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class:NSBS subsetting-utils
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class:Pairs Pairs-class
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class:RectangularData RectangularData-class
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class:Rle Rle-class
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class:SelfHits Hits-class
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class:SelfHitsList HitsList-class
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class:SimpleList SimpleList-class
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class:SortedByQueryHits Hits-class
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class:SortedByQueryHitsList HitsList-class
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class:SortedByQuerySelfHits Hits-class
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class:SortedByQuerySelfHitsList HitsList-class
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class:TransposedDataFrame TransposedDataFrame-class
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class:Vector Vector-class
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class:vector_OR_factor S4Vectors-internals
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class:vector_OR_Vector Vector-class
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classNameForDisplay show-utils
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classNameForDisplay,ANY-method show-utils
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classNameForDisplay,DFrame-method DataFrame-class
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classNameForDisplay,SimpleList-method SimpleList-class
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classNameForDisplay,SortedByQueryHits-method Hits-class
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coerce,ANY,AsIs-method S4Vectors-internals
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coerce,ANY,DataFrame-method DataFrame-class
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coerce,ANY,DataFrame_OR_NULL-method DataFrame-class
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coerce,ANY,DFrame-method DataFrame-class
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coerce,ANY,FilterRules-method FilterRules-class
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coerce,ANY,List-method List-class
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coerce,ANY,Rle-method Rle-class
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coerce,ANY,SimpleList-method SimpleList-class
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coerce,ANY,TransposedDataFrame-method TransposedDataFrame-class
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coerce,ANY,vector-method S4Vectors-internals
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coerce,AsIs,DFrame-method DataFrame-class
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coerce,character,LLint-method LLint-class
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coerce,data.frame,DFrame-method DataFrame-class
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coerce,data.table,DFrame-method DataFrame-class
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coerce,DataFrame,TransposedDataFrame-method TransposedDataFrame-class
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coerce,factor,Factor-method Factor-class
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coerce,function,FilterClosure-method FilterRules-class
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coerce,Hits,DFrame-method Hits-class
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coerce,Hits,SelfHits-method Hits-class
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coerce,Hits,SortedByQueryHits-method Hits-class
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coerce,Hits,SortedByQuerySelfHits-method Hits-class
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coerce,HitsList,SortedByQueryHitsList-method HitsList-class
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coerce,integer,List-method List-class
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coerce,integer,LLint-method LLint-class
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coerce,list,DFrame-method DataFrame-class
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coerce,List,list-method List-class
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coerce,list,List-method SimpleList-class
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coerce,list_OR_List,Pairs-method Pairs-class
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coerce,logical,LLint-method LLint-class
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coerce,NULL,DFrame-method DataFrame-class
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coerce,numeric,LLint-method LLint-class
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coerce,Pairs,DFrame-method Pairs-class
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coerce,Rle,character-method Rle-class
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coerce,Rle,complex-method Rle-class
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coerce,Rle,factor-method Rle-class
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coerce,Rle,integer-method Rle-class
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coerce,Rle,list-method Rle-class
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coerce,Rle,logical-method Rle-class
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coerce,Rle,numeric-method Rle-class
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coerce,Rle,raw-method Rle-class
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coerce,Rle,vector-method Rle-class
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coerce,SelfHits,SortedByQuerySelfHits-method Hits-class
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coerce,SimpleList,DataFrame-method DataFrame-class
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coerce,SimpleList,DFrame-method DataFrame-class
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coerce,SimpleList,FilterRules-method FilterRules-class
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coerce,SortedByQueryHits,SortedByQuerySelfHits-method Hits-class
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coerce,SortedByQueryHitsList,HitsList-method HitsList-class
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coerce,standardGeneric,FilterClosure-method FilterRules-class
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coerce,table,DFrame-method DataFrame-class
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coerce,TransposedDataFrame,DataFrame-method TransposedDataFrame-class
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coerce,Vector,character-method Vector-class
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coerce,Vector,complex-method Vector-class
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coerce,Vector,data.frame-method Vector-class
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coerce,Vector,DFrame-method DataFrame-class
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coerce,Vector,double-method Vector-class
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coerce,Vector,factor-method Vector-class
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coerce,Vector,integer-method Vector-class
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coerce,Vector,logical-method Vector-class
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coerce,Vector,numeric-method Vector-class
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coerce,Vector,raw-method Vector-class
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coerce,Vector,vector-method Vector-class
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coerce,vector_OR_Vector,Factor-method Factor-class
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coerce,xtabs,DFrame-method DataFrame-class
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colnames,DataFrame-method DataFrame-class
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colnames,TransposedDataFrame-method TransposedDataFrame-class
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colnames<-,DataFrame-method DataFrame-class
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combineCols RectangularData-class
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combineCols,DataFrame-method DataFrame-combine
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combineRows RectangularData-class
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combineRows,DataFrame-method DataFrame-combine
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combineUniqueCols RectangularData-class
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complete.cases,DataFrame-method DataFrame-utils
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Complex,Rle-method Rle-utils
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coolcat show-utils
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cor,Rle,Rle-method Rle-utils
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countLnodeHits Hits-class
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countLnodeHits,Hits-method Hits-class
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countMatches Vector-comparison
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countMatches,ANY,ANY-method Vector-comparison
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countQueryHits Hits-class
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countRnodeHits Hits-class
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countRnodeHits,Hits-method Hits-class
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countSubjectHits Hits-class
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cov,Rle,Rle-method Rle-utils
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DataFrame DataFrame-class
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DataFrame-class DataFrame-class
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DataFrame-combine DataFrame-combine
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DataFrame-utils DataFrame-utils
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DataFrameFactor DataFrameFactor-class
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DataFrameFactor-class DataFrameFactor-class
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DataFrame_OR_NULL S4Vectors-internals
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DataFrame_OR_NULL-class S4Vectors-internals
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decode Rle-class
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decode,ANY-method Rle-class
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decode,Rle-method Rle-class
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DFrame DataFrame-class
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DFrame-class DataFrame-class
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diff,Rle-method Rle-utils
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diff.Rle Rle-utils
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dim,DataFrameFactor-method DataFrameFactor-class
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dim,RectangularData-method RectangularData-class
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dimnames,DataFrameFactor-method DataFrameFactor-class
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dimnames,RectangularData-method RectangularData-class
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dimnames<-,DataFrame-method DataFrame-class
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dimnames<-,RectangularData-method RectangularData-class
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dimnames<-,TransposedDataFrame-method TransposedDataFrame-class
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droplevels,DFrame-method DataFrame-class
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droplevels,Factor-method Factor-class
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droplevels,List-method List-utils
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droplevels,Rle-method Rle-utils
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droplevels.Factor Factor-class
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droplevels.List List-utils
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droplevels.Rle Rle-utils
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duplicated,DataFrame-method DataFrame-comparison
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duplicated,Rle-method Rle-class
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duplicated,Vector-method Vector-comparison
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duplicated.DataFrame DataFrame-comparison
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duplicated.Vector Vector-comparison
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duplicatedIntegerPairs integer-utils
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duplicatedIntegerQuads integer-utils
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elementMetadata Vector-class
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elementMetadata,Vector-method Vector-class
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elementMetadata<- Vector-class
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elementMetadata<-,Vector-method Vector-class
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elementNROWS List-class
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elementNROWS,ANY-method List-class
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elementNROWS,List-method List-class
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elementType List-class
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elementType,List-method List-class
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elementType,vector-method List-class
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end,Rle-method Rle-class
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endoapply List-utils
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eval,FilterRules,ANY-method FilterRules-class
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evalSeparately FilterRules-class
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evalSeparately,FilterRules-method FilterRules-class
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expand expand-methods
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expand,DataFrame-method expand-methods
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expand,Vector-method expand-methods
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expand.grid Vector-class
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expand.grid,Vector-method Vector-class
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expression_OR_function FilterRules-class
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expression_OR_function-class FilterRules-class
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extractCOLS subsetting-utils
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extractCOLS,DataFrame-method DataFrame-class
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extractCOLS,TransposedDataFrame-method TransposedDataFrame-class
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extractROWS subsetting-utils
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extractROWS,ANY,ANY-method subsetting-utils
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extractROWS,array,RangeNSBS-method subsetting-utils
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extractROWS,data.frame,RangeNSBS-method subsetting-utils
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extractROWS,DataFrame,ANY-method DataFrame-class
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extractROWS,Rle,ANY-method Rle-class
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extractROWS,Rle,NSBS-method Rle-class
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extractROWS,Rle,RangeNSBS-method Rle-class
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extractROWS,Rle,RleNSBS-method Rle-class
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extractROWS,SortedByQueryHits,ANY-method Hits-class
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extractROWS,TransposedDataFrame,ANY-method TransposedDataFrame-class
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extractROWS,vector_OR_factor,RangeNSBS-method subsetting-utils
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Factor Factor-class
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Factor-class Factor-class
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FactorToClass Factor-class
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FactorToClass,vector_OR_Vector-method Factor-class
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Filter,List-method List-utils
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FilterMatrix FilterMatrix-class
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FilterMatrix-class FilterMatrix-class
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FilterRules FilterRules-class
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filterRules FilterMatrix-class
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filterRules,FilterMatrix-method FilterMatrix-class
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FilterRules-class FilterRules-class
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Find,List-method List-utils
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findMatches Vector-comparison
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findMatches,ANY,ANY-method Vector-comparison
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findMatches,ANY,missing-method Vector-comparison
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findRun Rle-class
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findRun,Rle-method Rle-class
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first Pairs-class
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first,Pairs-method Pairs-class
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first<- Pairs-class
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first<-,Pairs-method Pairs-class
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fold S4Vectors-internals
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from Hits-class
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from,Hits-method Hits-class
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getListElement subsetting-utils
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getListElement,DataFrame-method DataFrame-class
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getListElement,List-method List-class
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getListElement,list-method subsetting-utils
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getListElement,TransposedDataFrame-method TransposedDataFrame-class
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get_showHeadLines show-utils
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get_showTailLines show-utils
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gsub,ANY,ANY,Rle-method Rle-utils
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head Vector-class
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head,RectangularData-method RectangularData-class
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head,Vector-method Vector-class
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head.RectangularData RectangularData-class
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head.Vector Vector-class
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Hits Hits-class
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Hits-class Hits-class
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Hits-comparison Hits-comparison
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Hits-setops Hits-setops
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HitsList HitsList-class
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HitsList-class HitsList-class
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horizontal_slot_names RectangularData-class
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horizontal_slot_names,DFrame-method DataFrame-class
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integer_OR_LLint LLint-class
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integer_OR_LLint-class LLint-class
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integer_OR_raw Factor-class
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integer_OR_raw-class Factor-class
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intersect,ANY,Rle-method Rle-class
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intersect,Rle,ANY-method Rle-class
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intersect,Rle,Rle-method Rle-class
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intersect,Vector,Vector-method Vector-setops
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intersect.Vector Vector-setops
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IQR,Rle-method Rle-utils
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is.finite,Rle-method Rle-class
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is.LLint LLint-class
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is.na,DataFrame-method DataFrame-utils
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is.na,LLint-method LLint-class
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is.na,Rle-method Rle-class
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is.na,Vector-method Vector-class
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is.unsorted,Rle-method Rle-class
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isConstant isSorted
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isConstant,array-method isSorted
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isConstant,integer-method isSorted
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isConstant,numeric-method isSorted
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isEmpty List-class
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isEmpty,ANY-method List-class
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isEmpty,List-method List-class
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isRedundantHit Hits-class
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isSelfHit Hits-class
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isSequence integer-utils
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isSingleInteger S4Vectors-internals
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isSingleNumber S4Vectors-internals
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isSingleNumberOrNA S4Vectors-internals
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isSingleString S4Vectors-internals
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isSingleStringOrNA S4Vectors-internals
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isSorted isSorted
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isSorted,ANY-method isSorted
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isStrictlySorted isSorted
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isStrictlySorted,ANY-method isSorted
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isStrictlySorted,NSBS-method subsetting-utils
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isStrictlySorted,RangeNSBS-method subsetting-utils
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isStrictlySorted,Rle-method Rle-class
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isStrictlySorted,RleNSBS-method Rle-class
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isTRUEorFALSE S4Vectors-internals
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lapply,List-method List-utils
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lapply,SimpleList-method SimpleList-class
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length,DataFrame-method DataFrame-class
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length,LLint-method LLint-class
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length,NSBS-method subsetting-utils
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length,RangeNSBS-method subsetting-utils
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length,Rle-method Rle-class
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length,RleNSBS-method Rle-class
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|
length,TransposedDataFrame-method TransposedDataFrame-class
|
|
length,Vector-method Vector-class
|
|
lengths,Vector-method Vector-class
|
|
levels Factor-class
|
|
levels,Rle-method Rle-utils
|
|
levels.Rle Rle-utils
|
|
levels<- Factor-class
|
|
levels<-,Factor-method Factor-class
|
|
levels<-,Rle-method Rle-utils
|
|
List List-class
|
|
List-class List-class
|
|
List-utils List-utils
|
|
list_OR_List List-class
|
|
list_OR_List-class List-class
|
|
LLint LLint-class
|
|
LLint-class LLint-class
|
|
mad,Rle-method Rle-utils
|
|
mad.Rle Rle-utils
|
|
makeClassinfoRowForCompactPrinting show-utils
|
|
makeNakedCharacterMatrixForDisplay show-utils
|
|
makeNakedCharacterMatrixForDisplay,ANY-method show-utils
|
|
makeNakedCharacterMatrixForDisplay,DataFrame-method DataFrame-class
|
|
makeNakedCharacterMatrixForDisplay,Hits-method Hits-class
|
|
makeNakedCharacterMatrixForDisplay,Pairs-method Pairs-class
|
|
makeNakedCharacterMatrixForDisplay,TransposedDataFrame-method TransposedDataFrame-class
|
|
makePrettyMatrixForCompactPrinting show-utils
|
|
make_zero_col_DFrame DataFrame-class
|
|
Map,List-method List-utils
|
|
match Vector-comparison
|
|
match,ANY,Rle-method Rle-class
|
|
match,DataFrame,DataFrame-method DataFrame-comparison
|
|
match,Factor,Factor-method Factor-class
|
|
match,Hits,Hits-method Hits-comparison
|
|
match,Pairs,Pairs-method Pairs-class
|
|
match,Rle,ANY-method Rle-class
|
|
match,Rle,Rle-method Rle-class
|
|
match,Vector,Vector-method Vector-comparison
|
|
matchIntegerPairs integer-utils
|
|
matchIntegerQuads integer-utils
|
|
Math,Rle-method Rle-utils
|
|
Math2,Rle-method Rle-utils
|
|
max,NSBS-method subsetting-utils
|
|
max,RangeNSBS-method subsetting-utils
|
|
mcols Vector-class
|
|
mcols,Vector-method Vector-class
|
|
mcols<- Vector-class
|
|
mcols<-,Vector-method Vector-class
|
|
mean,Rle-method Rle-utils
|
|
mean.Rle Rle-utils
|
|
median,Rle-method Rle-utils
|
|
median.Rle Rle-utils
|
|
mendoapply List-utils
|
|
merge Vector-merge
|
|
merge,data.frame,DataFrame-method DataFrame-combine
|
|
merge,DataFrame,data.frame-method DataFrame-combine
|
|
merge,DataFrame,DataFrame-method DataFrame-combine
|
|
merge,Vector,Vector-method Vector-merge
|
|
mergeROWS subsetting-utils
|
|
mergeROWS,ANY,ANY-method subsetting-utils
|
|
mergeROWS,DFrame-method DataFrame-class
|
|
mergeROWS,Vector,ANY-method Vector-class
|
|
metadata Annotated-class
|
|
metadata,Annotated-method Annotated-class
|
|
metadata<- Annotated-class
|
|
metadata<-,Annotated-method Annotated-class
|
|
mstack stack-methods
|
|
mstack,DataFrame-method stack-methods
|
|
mstack,Vector-method stack-methods
|
|
mstack,vector-method stack-methods
|
|
na.exclude,DataFrame-method DataFrame-utils
|
|
na.omit,DataFrame-method DataFrame-utils
|
|
names,DataFrame-method DataFrame-class
|
|
names,Factor-method Factor-class
|
|
names,Pairs-method Pairs-class
|
|
names,SimpleList-method SimpleList-class
|
|
names,TransposedDataFrame-method TransposedDataFrame-class
|
|
names<-,Factor-method Factor-class
|
|
names<-,Pairs-method Pairs-class
|
|
names<-,SimpleList-method SimpleList-class
|
|
names<-,TransposedDataFrame-method TransposedDataFrame-class
|
|
NA_LLint_ LLint-class
|
|
nchar,Rle-method Rle-utils
|
|
ncol,DataFrame-method DataFrame-class
|
|
ncol,TransposedDataFrame-method TransposedDataFrame-class
|
|
new2 S4Vectors-internals
|
|
nlevels Factor-class
|
|
nlevels,Factor-method Factor-class
|
|
nLnode Hits-class
|
|
nLnode,Hits-method Hits-class
|
|
nnode Hits-class
|
|
nnode,SelfHits-method Hits-class
|
|
normalizeDoubleBracketSubscript subsetting-utils
|
|
normalizeSingleBracketReplacementValue subsetting-utils
|
|
normalizeSingleBracketReplacementValue,ANY-method subsetting-utils
|
|
normalizeSingleBracketReplacementValue,TransposedDataFrame-method TransposedDataFrame-class
|
|
normalizeSingleBracketSubscript subsetting-utils
|
|
nRnode Hits-class
|
|
nRnode,Hits-method Hits-class
|
|
nrow,DataFrame-method DataFrame-class
|
|
nrow,TransposedDataFrame-method TransposedDataFrame-class
|
|
nrun Rle-class
|
|
nrun,Rle-method Rle-class
|
|
NSBS subsetting-utils
|
|
NSBS,ANY-method subsetting-utils
|
|
NSBS,character-method subsetting-utils
|
|
NSBS,factor-method subsetting-utils
|
|
NSBS,logical-method subsetting-utils
|
|
NSBS,missing-method subsetting-utils
|
|
NSBS,NSBS-method subsetting-utils
|
|
NSBS,NULL-method subsetting-utils
|
|
NSBS,numeric-method subsetting-utils
|
|
NSBS,Rle-method Rle-class
|
|
NSBS-class subsetting-utils
|
|
Ops,LLint,LLint-method LLint-class
|
|
Ops,LLint,numeric-method LLint-class
|
|
Ops,numeric,LLint-method LLint-class
|
|
Ops,Rle,Rle-method Rle-utils
|
|
Ops,Rle,vector-method Rle-utils
|
|
Ops,vector,Rle-method Rle-utils
|
|
order,DataFrame-method DataFrame-comparison
|
|
order,Hits-method Hits-comparison
|
|
order,Pairs-method Pairs-class
|
|
order,Rle-method Rle-class
|
|
orderIntegerPairs integer-utils
|
|
orderIntegerQuads integer-utils
|
|
Pairs Pairs-class
|
|
Pairs-class Pairs-class
|
|
parallelVectorNames Vector-class
|
|
parallelVectorNames,ANY-method Vector-class
|
|
parallelVectorNames,List-method List-class
|
|
parallel_slot_names Vector-class
|
|
parallel_slot_names,Factor-method Factor-class
|
|
parallel_slot_names,FilterRules-method FilterRules-class
|
|
parallel_slot_names,Hits-method Hits-class
|
|
parallel_slot_names,Pairs-method Pairs-class
|
|
parallel_slot_names,SimpleList-method SimpleList-class
|
|
parallel_slot_names,Vector-method Vector-class
|
|
params FilterRules-class
|
|
params,FilterClosure-method FilterRules-class
|
|
paste,Rle-method Rle-utils
|
|
pc List-utils
|
|
pcompare Vector-comparison
|
|
pcompare,ANY,ANY-method Vector-comparison
|
|
pcompare,DataFrame,DataFrame-method DataFrame-comparison
|
|
pcompare,Factor,Factor-method Factor-class
|
|
pcompare,Hits,Hits-method Hits-comparison
|
|
pcompare,numeric,numeric-method Vector-comparison
|
|
pcompare,Pairs,Pairs-method Pairs-class
|
|
pmax,Rle-method Rle-utils
|
|
pmax.int,Rle-method Rle-utils
|
|
pmin,Rle-method Rle-utils
|
|
pmin.int,Rle-method Rle-utils
|
|
Position,List-method List-utils
|
|
printAtomicVectorInAGrid show-utils
|
|
quantile,Rle-method Rle-utils
|
|
quantile.Rle Rle-utils
|
|
queryHits Hits-class
|
|
queryHits,HitsList-method HitsList-class
|
|
queryLength Hits-class
|
|
rank,Rle-method Rle-class
|
|
rank,Vector-method Vector-comparison
|
|
rbind,FilterMatrix-method FilterMatrix-class
|
|
rbind,List-method List-utils
|
|
rbind,RectangularData-method RectangularData-class
|
|
rbind.RectangularData RectangularData-class
|
|
RectangularData RectangularData-class
|
|
RectangularData-class RectangularData-class
|
|
recycleArg S4Vectors-internals
|
|
recycleCharacterArg S4Vectors-internals
|
|
recycleIntegerArg S4Vectors-internals
|
|
recycleLogicalArg S4Vectors-internals
|
|
recycleNumericArg S4Vectors-internals
|
|
Reduce,List-method List-utils
|
|
relistToClass splitAsList
|
|
relistToClass,ANY-method splitAsList
|
|
relistToClass,data.frame-method DataFrame-utils
|
|
relistToClass,DataFrame-method DataFrame-utils
|
|
relistToClass,Hits-method HitsList-class
|
|
relistToClass,SortedByQueryHits-method HitsList-class
|
|
remapHits Hits-class
|
|
rename Vector-class
|
|
rename,Vector-method Vector-class
|
|
rename,vector-method Vector-class
|
|
rep Vector-class
|
|
rep,DataFrame-method DataFrame-class
|
|
rep,Rle-method Rle-class
|
|
rep,Vector-method Vector-class
|
|
rep.int Vector-class
|
|
rep.int,Rle-method Rle-class
|
|
rep.int,Vector-method Vector-class
|
|
replaceCOLS subsetting-utils
|
|
replaceCOLS,DFrame-method DataFrame-class
|
|
replaceROWS subsetting-utils
|
|
replaceROWS,ANY,ANY-method subsetting-utils
|
|
replaceROWS,DFrame-method DataFrame-class
|
|
replaceROWS,Rle,ANY-method Rle-class
|
|
replaceROWS,Vector,ANY-method Vector-class
|
|
rev Vector-class
|
|
rev,Rle-method Rle-class
|
|
rev,Vector-method Vector-class
|
|
rev.Rle Rle-class
|
|
rev.Vector Vector-class
|
|
revElements List-utils
|
|
revElements,List-method List-utils
|
|
revElements,list-method List-utils
|
|
Rle Rle-class
|
|
Rle,ANY-method Rle-class
|
|
Rle,Rle-method Rle-class
|
|
Rle-class Rle-class
|
|
Rle-runstat Rle-runstat
|
|
Rle-utils Rle-utils
|
|
ROWNAMES RectangularData-class
|
|
ROWNAMES,ANY-method RectangularData-class
|
|
rownames,DataFrame-method DataFrame-class
|
|
ROWNAMES,RectangularData-method RectangularData-class
|
|
rownames,TransposedDataFrame-method TransposedDataFrame-class
|
|
ROWNAMES<- RectangularData-class
|
|
ROWNAMES<-,ANY-method RectangularData-class
|
|
rownames<-,DFrame-method DataFrame-class
|
|
ROWNAMES<-,RectangularData-method RectangularData-class
|
|
runLength Rle-class
|
|
runLength,Rle-method Rle-class
|
|
runLength<- Rle-class
|
|
runLength<-,Rle-method Rle-class
|
|
runmean Rle-runstat
|
|
runmean,Rle-method Rle-runstat
|
|
runmed,Rle-method Rle-runstat
|
|
runq Rle-runstat
|
|
runq,Rle-method Rle-runstat
|
|
runsum Rle-runstat
|
|
runsum,Rle-method Rle-runstat
|
|
runValue Rle-class
|
|
runValue,Rle-method Rle-class
|
|
runValue<- Rle-class
|
|
runValue<-,Rle-method Rle-class
|
|
runwtsum Rle-runstat
|
|
runwtsum,Rle-method Rle-runstat
|
|
safeExplode character-utils
|
|
sameAsPreviousROW Vector-comparison
|
|
sameAsPreviousROW,ANY-method Vector-comparison
|
|
sameAsPreviousROW,DataFrame-method DataFrame-comparison
|
|
sameAsPreviousROW,Pairs-method Pairs-class
|
|
sapply,List-method List-utils
|
|
sd,Rle-method Rle-utils
|
|
second Pairs-class
|
|
second,Pairs-method Pairs-class
|
|
second<- Pairs-class
|
|
second<-,Pairs-method Pairs-class
|
|
selectHits Hits-class
|
|
SelfHits Hits-class
|
|
SelfHits-class Hits-class
|
|
SelfHitsList HitsList-class
|
|
SelfHitsList-class HitsList-class
|
|
selfmatch Vector-comparison
|
|
selfmatch,ANY-method Vector-comparison
|
|
selfmatch,Factor-method Factor-class
|
|
selfmatch,factor-method Vector-comparison
|
|
selfmatch,Vector-method Vector-comparison
|
|
selfmatchIntegerPairs integer-utils
|
|
selfmatchIntegerQuads integer-utils
|
|
setdiff,ANY,Rle-method Rle-class
|
|
setdiff,Rle,ANY-method Rle-class
|
|
setdiff,Rle,Rle-method Rle-class
|
|
setdiff,Vector,Vector-method Vector-setops
|
|
setdiff.Vector Vector-setops
|
|
setequal,Vector,Vector-method Vector-setops
|
|
setequal.Vector Vector-setops
|
|
setListElement subsetting-utils
|
|
setListElement,List-method List-class
|
|
setListElement,list-method subsetting-utils
|
|
setMethods S4Vectors-internals
|
|
setValidity2 S4Vectors-internals
|
|
set_showHeadLines show-utils
|
|
set_showTailLines show-utils
|
|
shiftApply shiftApply-methods
|
|
shiftApply,Vector,Vector-method shiftApply-methods
|
|
shiftApply,vector,vector-method shiftApply-methods
|
|
shiftApply-methods shiftApply-methods
|
|
show,DataFrame-method DataFrame-class
|
|
show,DataFrameFactor-method DataFrameFactor-class
|
|
show,Factor-method Factor-class
|
|
show,FilterClosure-method FilterRules-class
|
|
show,FilterMatrix-method FilterMatrix-class
|
|
show,Hits-method Hits-class
|
|
show,List-method List-class
|
|
show,LLint-method LLint-class
|
|
show,Pairs-method Pairs-class
|
|
show,RangeNSBS-method subsetting-utils
|
|
show,Rle-method Rle-class
|
|
show,TransposedDataFrame-method TransposedDataFrame-class
|
|
show-utils show-utils
|
|
showAsCell show-utils
|
|
showAsCell,ANY-method show-utils
|
|
showAsCell,AsIs-method show-utils
|
|
showAsCell,character-method show-utils
|
|
showAsCell,data.frame-method show-utils
|
|
showAsCell,DataFrame-method DataFrame-class
|
|
showAsCell,Factor-method Factor-class
|
|
showAsCell,List-method List-class
|
|
showAsCell,list-method show-utils
|
|
showAsCell,LLint-method LLint-class
|
|
showAsCell,numeric-method show-utils
|
|
showHeadLines show-utils
|
|
showTailLines show-utils
|
|
SimpleList SimpleList-class
|
|
SimpleList-class SimpleList-class
|
|
smoothEnds,Rle-method Rle-runstat
|
|
sort,DataFrame-method DataFrame-comparison
|
|
sort,Rle-method Rle-class
|
|
sort,SortedByQueryHits-method Hits-class
|
|
sort,Vector-method Vector-comparison
|
|
sort.DataFrame DataFrame-comparison
|
|
sort.Rle Rle-class
|
|
sort.Vector Vector-comparison
|
|
SortedByQueryHits Hits-class
|
|
SortedByQueryHits-class Hits-class
|
|
SortedByQueryHitsList HitsList-class
|
|
SortedByQueryHitsList-class HitsList-class
|
|
SortedByQuerySelfHits Hits-class
|
|
SortedByQuerySelfHits-class Hits-class
|
|
SortedByQuerySelfHitsList HitsList-class
|
|
SortedByQuerySelfHitsList-class HitsList-class
|
|
space HitsList-class
|
|
space,HitsList-method HitsList-class
|
|
split splitAsList
|
|
split,ANY,Vector-method splitAsList
|
|
split,list,Vector-method splitAsList
|
|
split,Vector,ANY-method splitAsList
|
|
split,Vector,Vector-method splitAsList
|
|
splitAsList splitAsList
|
|
splitAsList,ANY,ANY-method splitAsList
|
|
splitAsList,SortedByQueryHits,ANY-method HitsList-class
|
|
stack,List-method stack-methods
|
|
stack,matrix-method stack-methods
|
|
stack-methods stack-methods
|
|
start,Rle-method Rle-class
|
|
sub,ANY,ANY,Rle-method Rle-utils
|
|
subjectHits Hits-class
|
|
subjectHits,HitsList-method HitsList-class
|
|
subjectLength Hits-class
|
|
subset Vector-class
|
|
subset,RectangularData-method RectangularData-class
|
|
subset,Vector-method Vector-class
|
|
subset.Vector Vector-class
|
|
subsetByFilter FilterRules-class
|
|
subsetByFilter,ANY,FilterRules-method FilterRules-class
|
|
subsetting-utils subsetting-utils
|
|
substr,Rle-method Rle-utils
|
|
substring,Rle-method Rle-utils
|
|
summary,FilterMatrix-method FilterMatrix-class
|
|
summary,FilterRules-method FilterRules-class
|
|
summary,Hits-method Hits-class
|
|
Summary,LLint-method LLint-class
|
|
Summary,Rle-method Rle-utils
|
|
summary,Rle-method Rle-utils
|
|
summary,Vector-method Vector-class
|
|
summary.Hits Hits-class
|
|
summary.Rle Rle-utils
|
|
summary.Vector Vector-class
|
|
svn.time character-utils
|
|
t,DataFrame-method TransposedDataFrame-class
|
|
t,Hits-method Hits-class
|
|
t,HitsList-method HitsList-class
|
|
t,TransposedDataFrame-method TransposedDataFrame-class
|
|
t.DataFrame TransposedDataFrame-class
|
|
t.Hits Hits-class
|
|
t.TransposedDataFrame TransposedDataFrame-class
|
|
table,Rle-method Rle-class
|
|
table,Vector-method Vector-comparison
|
|
tabulate,Rle-method Rle-class
|
|
tail Vector-class
|
|
tail,RectangularData-method RectangularData-class
|
|
tail,Vector-method Vector-class
|
|
tail.RectangularData RectangularData-class
|
|
tail.Vector Vector-class
|
|
to Hits-class
|
|
to,Hits-method Hits-class
|
|
toListOfIntegerVectors integer-utils
|
|
tolower,Rle-method Rle-utils
|
|
toupper,Rle-method Rle-utils
|
|
transform,DataFrame-method DataFrame-utils
|
|
transform,Vector-method Vector-class
|
|
transform.DataFrame DataFrame-utils
|
|
transform.Vector Vector-class
|
|
TransposedDataFrame TransposedDataFrame-class
|
|
TransposedDataFrame-class TransposedDataFrame-class
|
|
unfactor Factor-class
|
|
unfactor,Factor-method Factor-class
|
|
unfactor,factor-method Factor-class
|
|
union,ANY,Rle-method Rle-class
|
|
union,Rle,ANY-method Rle-class
|
|
union,Rle,Rle-method Rle-class
|
|
union,SortedByQueryHits,Hits-method Hits-setops
|
|
union,Vector,Vector-method Vector-setops
|
|
union.Vector Vector-setops
|
|
unique,DataFrame-method DataFrame-comparison
|
|
unique,Rle-method Rle-class
|
|
unique,Vector-method Vector-comparison
|
|
unique.DataFrame DataFrame-comparison
|
|
unique.Vector Vector-comparison
|
|
unlist,List-method List-class
|
|
unname,Vector-method Vector-class
|
|
unstrsplit character-utils
|
|
unstrsplit,character-method character-utils
|
|
unstrsplit,list-method character-utils
|
|
updateObject,DataFrame-method DataFrame-class
|
|
updateObject,Hits-method Hits-class
|
|
updateObject,SimpleList-method SimpleList-class
|
|
updateObject,Vector-method Vector-class
|
|
values Vector-class
|
|
values,Vector-method Vector-class
|
|
values<- Vector-class
|
|
values<-,Vector-method Vector-class
|
|
var,Rle,missing-method Rle-utils
|
|
var,Rle,Rle-method Rle-utils
|
|
Vector Vector-class
|
|
Vector-class Vector-class
|
|
Vector-comparison Vector-comparison
|
|
Vector-merge Vector-merge
|
|
Vector-setops Vector-setops
|
|
vector_OR_factor S4Vectors-internals
|
|
vector_OR_factor-class S4Vectors-internals
|
|
vector_OR_Vector Vector-class
|
|
vector_OR_Vector-class Vector-class
|
|
vertical_slot_names RectangularData-class
|
|
vertical_slot_names,DFrame-method DataFrame-class
|
|
which,Rle-method Rle-utils
|
|
which.max,Rle-method Rle-utils
|
|
width,Rle-method Rle-class
|
|
window Vector-class
|
|
window,Vector-method Vector-class
|
|
window.Vector Vector-class
|
|
within,List-method List-utils
|
|
wmsg S4Vectors-internals
|
|
xtabs,DataFrame-method DataFrame-utils
|
|
xtfrm,Factor-method Factor-class
|
|
xtfrm,Rle-method Rle-class
|
|
xtfrm,Vector-method Vector-comparison
|
|
zipdown zip-methods
|
|
zipdown,ANY-method zip-methods
|
|
zipdown,List-method zip-methods
|
|
zipup zip-methods
|
|
zipup,ANY,ANY-method zip-methods
|
|
zipup,Pairs,missing-method Pairs-class
|
|
[ Vector-class
|
|
[,DataFrame-method DataFrame-class
|
|
[,DataFrameFactor,ANY,ANY,ANY-method DataFrameFactor-class
|
|
[,DataFrameFactor-method DataFrameFactor-class
|
|
[,FilterMatrix-method FilterMatrix-class
|
|
[,FilterRules-method FilterRules-class
|
|
[,List-method List-class
|
|
[,Rle-method Rle-class
|
|
[,TransposedDataFrame-method TransposedDataFrame-class
|
|
[,Vector-method Vector-class
|
|
[<-,DataFrame-method DataFrame-class
|
|
[<-,List-method List-class
|
|
[<-,Rle,ANY-method Rle-class
|
|
[<-,TransposedDataFrame-method TransposedDataFrame-class
|
|
[<-,Vector-method Vector-class
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[[,DataFrame-method DataFrame-class
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[[,DataFrameFactor,ANY,ANY-method DataFrameFactor-class
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[[,DataFrameFactor-method DataFrameFactor-class
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[[,DFrame-method DataFrame-class
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[[,List-method List-class
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[[<-,DFrame-method DataFrame-class
|
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[[<-,FilterRules-method FilterRules-class
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[[<-,List-method List-class
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