Entry: Alignment-class
Aliases: score score,AlignmentSpace-method
Keywords: classes
Description: Alignments between sequences
URL: ../../../library/IRanges/html/Alignment-class.html

Entry: AnnotatedList-class
Aliases: AnnotatedList-class metadata metadata,AnnotatedList-method elementMetadata elementMetadata,AnnotatedList-method metadata<- metadata<-,AnnotatedList,list-method elementMetadata<- elementMetadata<-,AnnotatedList,XDataFrameORNULL-method AnnotatedList
Keywords: methods classes
Description: Annotated Lists
URL: ../../../library/IRanges/html/AnnotatedList-class.html

Entry: AtomicList
Aliases: LogicalList LogicalList-class IntegerList IntegerList-class NumericList NumericList-class ComplexList ComplexList-class CharacterList CharacterList-class RawList RawList-class RleList RleList-class
Keywords: methods classes
Description: Lists of Atomic Vectors in Natural and Rle Form
URL: ../../../library/IRanges/html/AtomicList-class.html

Entry: FilterRules-class
Aliases: FilterRules-class active,FilterRules-method active<-,FilterRules-method [,FilterRules-method [[<-,FilterRules-method append,FilterRules,FilterRules-method c,FilterRules-method eval,FilterRules,ANY-method FilterRules
Keywords: classes methods
Description: Collection of Filter Rules
URL: ../../../library/IRanges/html/FilterRules-class.html

Entry: IRanges-class
Aliases: class:IRanges IRanges-class start,IRanges-method width,IRanges-method names,IRanges-method start<-,IRanges-method width<-,IRanges-method end<-,IRanges-method names<-,IRanges-method update,IRanges-method [,IRanges-method c,IRanges-method class:NormalIRanges NormalIRanges-class NormalIRanges isEmpty,NormalIRanges-method max,NormalIRanges-method min,NormalIRanges-method coerce,logical,IRanges-method coerce,logical,NormalIRanges-method
Keywords: methods classes
Description: IRanges and NormalIRanges objects
URL: ../../../library/IRanges/html/IRanges-class.html

Entry: IRanges-constructor
Aliases: IRanges-constructor IRanges solveUserSEW0 solveUserSEW
Keywords: utilities
Description: The IRanges constructor and supporting functions
URL: ../../../library/IRanges/html/IRanges-constructor.html

Entry: IRanges internals
Aliases: setValidity2 new2 sapplyLength safeExplode isTRUEorFALSE isSingleInteger isSingleNumber isSingleString isSingleIntegerOrNA isSingleNumberOrNA isSingleStringOrNA isConstant normargShift normargWeight class:characterORNULL characterORNULL-class characterORNULL coerce,ANY,vector-method class:SequencePtr SequencePtr-class SequencePtr as.numeric,SequencePtr-method show,externalptr-method length,SequencePtr-method ==,SequencePtr,SequencePtr-method !=,SequencePtr,SequencePtr-method class:RawPtr RawPtr-class RawPtr show,RawPtr-method RawPtr.readInts RawPtr.writeInts RawPtr.read RawPtr.write RawPtr.copy RawPtr.reverseCopy RawPtr.readComplexes RawPtr.append RawPtr.compare as.integer,RawPtr-method toString,RawPtr-method class:IntegerPtr IntegerPtr-class IntegerPtr show,IntegerPtr-method as.integer,IntegerPtr-method class:NumericPtr NumericPtr-class NumericPtr show,NumericPtr-method as.numeric,NumericPtr-method
Keywords: internal methods classes
Description: IRanges internals
URL: ../../../library/IRanges/html/IRanges-internals.html

Entry: IRanges-setops
Aliases: IRanges-setops union,IRanges,IRanges-method intersect,IRanges,IRanges-method setdiff,IRanges,IRanges-method punion punion,IRanges,IRanges-method pintersect pintersect,IRanges,IRanges-method psetdiff psetdiff,IRanges,IRanges-method pgap pgap,IRanges,IRanges-method
Keywords: utilities
Description: Set operations on IRanges objects
URL: ../../../library/IRanges/html/IRanges-setops.html

Entry: IRanges-utils
Aliases: IRanges-utils successiveIRanges whichAsIRanges shift shift,IRanges-method restrict restrict,IRanges-method narrow narrow,IRanges-method narrow,NormalIRanges-method threebands threebands,IRanges-method reduce reduce,IRanges-method gaps gaps,IRanges-method reflect reflect,Ranges-method flank flank,Ranges-method range,Ranges-method *,Ranges,numeric-method asNormalIRanges coerce,IRanges,NormalIRanges-method intToRanges intToAdjacentRanges toNormalIRanges
Keywords: utilities
Description: IRanges utility functions
URL: ../../../library/IRanges/html/IRanges-utils.html

Entry: IRangesList-class
Aliases: IRangesList-class coerce,IRangesList,NormalIRanges-method coerce,IRangesList,list-method unlist,IRangesList-method summary,IRangesList-method IRangesList
Keywords: classes methods
Description: List of IRanges
URL: ../../../library/IRanges/html/IRangesList-class.html

Entry: IntervalTree-class
Aliases: IntervalTree-class IntervalTree coerce,IRanges,IntervalTree-method coerce,Ranges,IntervalTree-method coerce,IntervalTree,IRanges-method length,IntervalTree-method overlap overlap,IntervalTree,Ranges-method overlap,Ranges,Ranges-method overlap,Ranges,missing-method overlap,Ranges,integer-method overlap,RangesList,RangesList-method %in%,Ranges,Ranges-method
Keywords: classes methods
Description: Interval Search Trees
URL: ../../../library/IRanges/html/IntervalTree-class.html

Entry: ListLike-class
Aliases: class:ListLike ListLike-class ListLike [[,ListLike-method $,ListLike-method lapply,ListLike-method sapply sapply,ListLike-method as.list,ListLike-method isEmpty isEmpty,ANY-method
Keywords: methods classes
Description: ListLike objects
URL: ../../../library/IRanges/html/ListLike-class.html

Entry: MaskCollection-class
Aliases: class:MaskCollection MaskCollection-class MaskCollection nir_list nir_list,MaskCollection-method length,MaskCollection-method width,MaskCollection-method active active,MaskCollection-method active<- active<-,MaskCollection-method names,MaskCollection-method names<-,MaskCollection-method desc desc,MaskCollection-method desc<- desc<-,MaskCollection-method Mask max,MaskCollection-method min,MaskCollection-method maskedwidth maskedwidth,MaskCollection-method maskedratio maskedratio,MaskCollection-method [[,MaskCollection-method [[<-,MaskCollection-method [,MaskCollection-method [<-,MaskCollection-method append,MaskCollection,MaskCollection-method reduce,MaskCollection-method gaps,MaskCollection-method subseq,MaskCollection-method coerce,MaskCollection,NormalIRanges-method MaskCollection.show_frame show,MaskCollection-method
Keywords: methods classes
Description: MaskCollection objects
URL: ../../../library/IRanges/html/MaskCollection-class.html

Entry: rdapply
Aliases: rdapply rdapply,RDApplyParams-method RDApplyParams-class RDApplyParams applyFun applyFun,RDApplyParams-method applyFun<- applyFun<-,RDApplyParams-method applyParams applyParams,RDApplyParams-method applyParams<- applyParams<-,RDApplyParams-method filterRules filterRules,RDApplyParams-method filterRules<- filterRules<-,RDApplyParams-method rangedData rangedData,RDApplyParams-method rangedData<- rangedData<-,RDApplyParams-method reducerFun reducerFun,RDApplyParams-method reducerFun<- reducerFun<-,RDApplyParams-method reducerParams reducerParams,RDApplyParams-method reducerParams<- reducerParams<-,RDApplyParams-method simplify simplify,RDApplyParams-method simplify<- simplify<-,RDApplyParams-method
Keywords: classes methods
Description: Applying over spaces
URL: ../../../library/IRanges/html/RDApplyParams-class.html

Entry: RangedData-class
Aliases: RangedData-class universe,RangedData-method dim,RangedData-method dimnames,RangedData-method dimnames<-,RangedData-method end,RangedData-method length,RangedData-method names,RangedData-method names<-,RangedData-method ranges ranges,RangedData-method start,RangedData-method values values,RangedData-method width,RangedData-method space,RangedData-method universe,RangedData-method universe<-,RangedData-method RangedData updateRangedData as.data.frame,RangedData-method coerce,RangedData,XDataFrame-method coerce,Rle,RangedData-method coerce,XRle,RangedData-method c,RangedData-method rbind,RangedData-method split,RangedData-method [,RangedData-method [<-,RangedData-method [[,RangedData-method [[<-,RangedData-method $,RangedData-method $<-,RangedData-method lapply,RangedData-method show,RangedData-method
Keywords: methods classes
Description: Data on ranges
URL: ../../../library/IRanges/html/RangedData-class.html

Entry: RangedData-utils
Aliases: RangedData-utils eval,expressionORlanguage,RangedData-method range,RangedData-method
Keywords: utilities
Description: RangedData utility functions
URL: ../../../library/IRanges/html/RangedData-utils.html

Entry: RangedDataList-class
Aliases: RangedDataList-class unlist,RangedDataList-method RangedDataList
Keywords: classes
Description: Lists of RangedData
URL: ../../../library/IRanges/html/RangedDataList-class.html

Entry: Ranges-class
Aliases: class:Ranges Ranges-class RangesORmissing-class Ranges length,Ranges-method width start,Ranges-method width,Ranges-method end,Ranges-method mid mid,Ranges-method start<- width<- end<- isEmpty,Ranges-method isDisjoint isDisjoint,Ranges-method as.matrix,Ranges-method as.data.frame,Ranges-method as.integer,Ranges-method show,Ranges-method [<-,Ranges-method rep,Ranges-method isNormal isNormal,Ranges-method whichFirstNotNormal whichFirstNotNormal,Ranges-method first first,Ranges-method last last,Ranges-method
Keywords: methods classes
Description: Ranges objects
URL: ../../../library/IRanges/html/Ranges-class.html

Entry: Ranges-comparison
Aliases: Ranges-comparison == ==,Ranges,Ranges-method != !=,Ranges,Ranges-method duplicated duplicated,Ranges-method unique unique,Ranges-method <= <=,Ranges,Ranges-method >= >=,Ranges,Ranges-method < <,Ranges,Ranges-method > >,Ranges,Ranges-method order order,Ranges-method sort sort,Ranges-method rank rank,Ranges-method
Keywords: methods
Description: Ranges comparison
URL: ../../../library/IRanges/html/Ranges-comparison.html

Entry: RangesList-class
Aliases: RangesList-class RangesList end,RangesList-method width,RangesList-method start,RangesList-method space space,RangesList-method universe,RangesList-method universe<-,RangesList-method universe universe<- [,RangesList-method as.data.frame,RangesList-method coerce,RangesList,IRangesList-method coerce,RangesList,RangedData-method Ops,RangesList,ANY-method show,RangesList-method split,Ranges-method
Keywords: methods classes
Description: List of Ranges
URL: ../../../library/IRanges/html/RangesList-class.html

Entry: RangesList-utils
Aliases: RangesList-utils reduce,RangesList-method gaps,RangesList-method range,RangesList-method
Keywords: utilities
Description: RangesList utility functions
URL: ../../../library/IRanges/html/RangesList-utils.html

Entry: RangesMatching-class
Aliases: RangesMatching-class matchMatrix matchMatrix,RangesMatching-method dim,RangesMatching-method ranges,RangesMatching-method length,RangesMatching-method as.matrix,RangesMatching-method as.table,RangesMatching-method t,RangesMatching-method
Keywords: methods classes
Description: Matchings between Ranges
URL: ../../../library/IRanges/html/RangesMatching-class.html

Entry: RangesMatchingList-class
Aliases: RangesMatchingList-class as.matrix,RangesMatchingList-method as.table,RangesMatchingList-method t,RangesMatchingList-method space,RangesMatchingList-method ranges,RangesMatchingList-method
Keywords: methods classes
Description: List of Matchings between Ranges
URL: ../../../library/IRanges/html/RangesMatchingList-class.html

Entry: Rle-class
Aliases: class:Rle Rle-class Rle Rle,missing,missing-method Rle,vectorORfactor,missing-method Rle,vectorORfactor,integer-method Rle,vectorORfactor,numeric-method runLength runLength,Rle-method runValue runValue,Rle-method nrun nrun,Rle-method start,Rle-method end,Rle-method width,Rle-method runLength<- runLength<-,Rle-method runValue<- runValue<-,Rle-method as.vector,Rle,missing-method as.logical,Rle-method as.integer,Rle-method as.numeric,Rle-method as.complex,Rle-method as.character,Rle-method as.raw,Rle-method as.factor,Rle-method coerce,vector,Rle-method coerce,factor,Rle-method coerce,Rle,vector-method coerce,Rle,logical-method coerce,Rle,integer-method coerce,Rle,numeric-method coerce,Rle,complex-method coerce,Rle,character-method coerce,Rle,raw-method coerce,Rle,factor-method coerce,Rle,IRanges-method coerce,Rle,NormalIRanges-method Ops,Rle,Rle-method Ops,Rle,vector-method Ops,vector,Rle-method Math,Rle-method Math2,Rle-method Summary,Rle-method Complex,Rle-method [,Rle-method %in%,Rle,ANY-method aggregate,Rle-method c,Rle-method findRange findRange,Rle-method findRun findRun,Rle-method head,Rle-method is.na,Rle-method length,Rle-method rep,Rle-method rep.int rep.int,Rle-method rev,Rle-method shiftApply shiftApply,Rle,Rle-method show,Rle-method sort,Rle-method subseq,Rle-method summary,Rle-method table table,Rle-method tail,Rle-method unique,Rle-method window,Rle-method !,Rle-method which,Rle-method pmax pmax,Rle-method pmin pmin,Rle-method pmax.int pmax.int,Rle-method pmin.int pmin.int,Rle-method diff,Rle-method mean,Rle-method var,Rle,missing-method var,Rle,Rle-method cov,Rle,Rle-method cor,Rle,Rle-method sd,Rle-method median,Rle-method quantile,Rle-method mad,Rle-method nchar,Rle-method substr,Rle-method substring,Rle-method chartr,ANY,ANY,Rle-method tolower,Rle-method toupper,Rle-method sub,ANY,ANY,Rle-method gsub,ANY,ANY,Rle-method
Keywords: methods classes
Description: Rle objects
URL: ../../../library/IRanges/html/Rle-class.html

Entry: RleViews-class
Aliases: class:RleViews RleViews-class RleViews Views,Rle-method show,RleViews-method
Keywords: methods classes
Description: The RleViews class
URL: ../../../library/IRanges/html/RleViews-class.html

Entry: Sequence-class
Aliases: class:Sequence Sequence-class Sequence subseq subseq<- subseq,vector-method subseq,Sequence-method subseq<-,ANY-method rep,Sequence-method [<-,Sequence-method !=,Sequence,Sequence-method class:XSequence XSequence-class XSequence length,XSequence-method subseq,XSequence-method as.numeric,XSequence-method show,XSequence-method class:XRaw XRaw-class XRaw coerce,raw,XRaw-method coerce,raw,XSequence-method coerce,numeric,XRaw-method as.raw,XRaw-method as.integer,XRaw-method as.vector,XRaw,missing-method [,XRaw-method c,XRaw-method class:XInteger XInteger-class XInteger coerce,numeric,XInteger-method coerce,integer,XSequence-method as.integer,XInteger-method as.vector,XInteger,missing-method [,XInteger-method ==,XInteger,XInteger-method class:XNumeric XNumeric-class XNumeric coerce,numeric,XNumeric-method coerce,numeric,XSequence-method as.numeric,XNumeric-method as.vector,XNumeric,missing-method [,XNumeric-method show,XNumeric-method ==,XNumeric,XNumeric-method class:XRle XRle-class XRle length,XRle-method rep,XRle-method reverse,XRle-method ==,XRle,XRle-method [,XRle-method subseq,XRle-method class:XRleInteger XRleInteger-class XRleInteger Arith,integer,XRleInteger-method Arith,XRleInteger,integer-method Arith,XRleInteger,XRleInteger-method as.integer,XRleInteger-method as.vector,XRleInteger,missing-method coerce,integer,XRleInteger-method show,XRleInteger-method
Keywords: methods classes
Description: Sequence objects
URL: ../../../library/IRanges/html/Sequence-class.html

Entry: TypedList-class
Aliases: TypedList-class updateTypedList elementClass elementClass,TypedList-method elementLengths elementLengths,TypedList-method length,TypedList-method names,TypedList-method names<-,TypedList-method [,TypedList-method [<-,TypedList-method [[,TypedList-method [[<-,TypedList-method $<-,TypedList-method append,TypedList,TypedList-method c,TypedList-method as.list,TypedList-method coerce,TypedList,list-method unlist,TypedList-method lapply,TypedList-method sapply,TypedList-method show,TypedList-method
Keywords: methods classes
Description: Typed Lists
URL: ../../../library/IRanges/html/TypedList-class.html

Entry: Views-class
Aliases: class:Views Views-class subject subject,Views-method newViews Views coerce,Sequence,Views-method [[,Views-method [[<-,Views-method coerce,Views,NormalIRanges-method restrict,Views-method trim trim,Views-method narrow,Views-method subviews subviews,Views-method gaps,Views-method successiveViews views
Keywords: methods classes
Description: Views objects
URL: ../../../library/IRanges/html/Views-class.html

Entry: Views-utils
Aliases: Views-utils slice slice,integer-method slice,Rle-method slice,XInteger-method slice,XRleInteger-method viewApply viewApply,Views-method viewApply,RleViews-method viewMins viewMins,RleViews-method viewMins,XIntegerViews-method viewMins,XRleIntegerViews-method viewMaxs viewMaxs,RleViews-method viewMaxs,XIntegerViews-method viewMaxs,XRleIntegerViews-method viewSums viewSums,RleViews-method viewSums,XIntegerViews-method viewSums,XRleIntegerViews-method viewWhichMins viewWhichMins,RleViews-method viewWhichMins,XIntegerViews-method viewWhichMins,XRleIntegerViews-method viewWhichMaxs viewWhichMaxs,RleViews-method viewWhichMaxs,XIntegerViews-method viewWhichMaxs,XRleIntegerViews-method viewRangeMins viewRangeMins,RleViews-method viewRangeMaxs viewRangeMaxs,RleViews-method
Keywords: methods algebra arith
Description: Utility functions and numeric summary of Views of numerics
URL: ../../../library/IRanges/html/Views-utils.html

Entry: XDataFrame-class
Aliases: XDataFrame-class dim,XDataFrame-method dimnames,XDataFrame-method dimnames<-,XDataFrame-method XDataFrame [,XDataFrame-method [[,XDataFrame-method [[<-,XDataFrame-method as.data.frame,XDataFrame-method coerce,ANY,XDataFrame-method coerce,matrix,XDataFrame-method coerce,list,XDataFrame-method coerce,integer,XDataFrame-method coerce,data.frame,XDataFrame-method coerce,XDataFrame,data.frame-method as.list,XDataFrame-method cbind cbind,XDataFrame-method rbind rbind,XDataFrame-method split,XDataFrame-method show,XDataFrame-method is.array,XDataFrame-method
Keywords: classes methods
Description: External Data Frame
URL: ../../../library/IRanges/html/XDataFrame-class.html

Entry: XDataFrame-utils
Aliases: XDataFrame-utils eval,expressionORlanguage,XDataFrame-method
Keywords: utilities
Description: XDataFrame utility functions
URL: ../../../library/IRanges/html/XDataFrame-utils.html

Entry: XDataFrameList-class
Aliases: XDataFrameList-class SplitXDataFrameList-class dim,XDataFrameList-method dimnames,XDataFrameList-method XDataFrameList SplitXDataFrameList as.data.frame,SplitXDataFrameList-method coerce,SplitXDataFrameList,XDataFrame-method
Keywords: methods classes
Description: List of XDataFrames
URL: ../../../library/IRanges/html/XDataFrameList-class.html

Entry: XIntegerViews-class
Aliases: class:XIntegerViews XIntegerViews-class XIntegerViews Views,XInteger-method Views,integer-method show,XIntegerViews-method [[,XIntegerViews-method [[<-,XIntegerViews-method ==,XIntegerViews,XIntegerViews-method ==,XIntegerViews,XInteger-method ==,XIntegerViews,integer-method ==,XInteger,XIntegerViews-method ==,integer,XIntegerViews-method !=,XIntegerViews,XIntegerViews-method !=,XIntegerViews,XInteger-method !=,XIntegerViews,integer-method !=,XInteger,XIntegerViews-method !=,integer,XIntegerViews-method
Keywords: methods classes
Description: The XIntegerViews class
URL: ../../../library/IRanges/html/XIntegerViews-class.html

Entry: XRanges-class
Aliases: XRanges-class XRanges end,XRanges-method start,XRanges-method width,XRanges-method gaps,XRanges-method reduce,XRanges-method
Keywords: methods classes
Description: External Ranges
URL: ../../../library/IRanges/html/XRanges-class.html

Entry: XRleIntegerViews-class
Aliases: class:XRleIntegerViews XRleIntegerViews-class XRleIntegerViews Views,XRleInteger-method show,XRleIntegerViews-method [[,XRleIntegerViews-method [[<-,XRleIntegerViews-method ==,XRleIntegerViews,XRleIntegerViews-method ==,XRleIntegerViews,XRleInteger-method ==,XRleIntegerViews,integer-method ==,XRleInteger,XRleIntegerViews-method ==,integer,XRleIntegerViews-method !=,XRleIntegerViews,XRleIntegerViews-method !=,XRleIntegerViews,XRleInteger-method !=,XRleIntegerViews,integer-method !=,XRleInteger,XRleIntegerViews-method !=,integer,XRleIntegerViews-method
Keywords: methods classes
Description: The XRleIntegerViews class
URL: ../../../library/IRanges/html/XRleIntegerViews-class.html

Entry: coverage
Aliases: coverage.isCalledWithStartEndInterface coverage.getShift0FromStartEnd coverage.getWidthFromStartEnd coverage.normargWidth coverage coverage,numeric-method coverage,IRanges-method coverage,Views-method coverage,MaskCollection-method
Keywords: methods
Description: Coverage across a set of ranges
URL: ../../../library/IRanges/html/coverage.html

Entry: disjoin
Aliases: disjoin disjointBins disjoin,Ranges-method disjointBins,Ranges-method
Keywords: utilities
Description: Making Ranges disjoint
URL: ../../../library/IRanges/html/disjoin.html

Entry: nearest
Aliases: nearest precede follow nearest,Ranges,RangesORmissing-method precede,Ranges,RangesORmissing-method follow,Ranges,RangesORmissing-method
Keywords: utilities
Description: Nearest neighbor finding
URL: ../../../library/IRanges/html/nearest.html

Entry: read.Mask
Aliases: read.Mask read.agpMask read.gapMask read.liftMask read.rmMask read.trfMask
Keywords: manip
Description: Read a mask from a file
URL: ../../../library/IRanges/html/read.Mask.html

Entry: reverse
Aliases: reverse reverse,IRanges-method reverse,NormalIRanges-method reverse,MaskCollection-method
Keywords: methods manip
Description: Reverse ranges
URL: ../../../library/IRanges/html/reverse.html
