Entry: FilterRules-class
Aliases: FilterRules-class active,FilterRules-method active<-,FilterRules-method [,FilterRules,ANY,ANY,ANY-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: GenomicData-class
Aliases: GenomicData-class GenomicData chrom chrom,GenomicData-method genome genome,GenomicData-method strand strand,GenomicData-method strand,missing-method coerce,XRle,GenomicData-method c,GenomicData-method
Keywords: classes methods
Description: Data on a Genome
URL: ../../../library/IRanges/html/GenomicData-class.html

Entry: IRanges-class
Aliases: class:IRanges IRanges-class IRanges 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,ANY,ANY,ANY-method c,IRanges-method class:NormalIRanges NormalIRanges-class NormalIRanges isEmpty,NormalIRanges-method max,NormalIRanges-method min,NormalIRanges-method
Keywords: methods classes
Description: IRanges and NormalIRanges objects
URL: ../../../library/IRanges/html/IRanges-class.html

Entry: IRanges internals
Aliases: setValidity2 new2 sapplyLength safeExplode isTRUEorFALSE isSingleInteger isSingleNumber isSingleString isSingleIntegerOrNA isSingleNumberOrNA isSingleStringOrNA class:characterORNULL characterORNULL-class characterORNULL class:ListLike ListLike-class ListLike [[,ListLike-method $,ListLike-method lapply,ListLike,ANY-method sapply sapply,ListLike-method as.list,ListLike-method class:SequencePtr SequencePtr-class SequencePtr 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
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 reduce reduce,IRanges-method gaps gaps,IRanges-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 unlist,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 %in%,Ranges,Ranges-method
Keywords: classes methods
Description: Interval Search Trees
URL: ../../../library/IRanges/html/IntervalTree-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 isEmpty,MaskCollection-method max,MaskCollection-method min,MaskCollection-method maskedwidth maskedwidth,MaskCollection-method maskedratio maskedratio,MaskCollection-method [[,MaskCollection-method [[<-,MaskCollection-method [,MaskCollection,ANY,ANY,ANY-method [<-,MaskCollection,ANY,ANY,ANY-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 annotation annotation,RangedData-method dim,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 RangedData as.data.frame,RangedData-method coerce,RangedData,XDataFrame-method coerce,XRle,RangedData-method c,RangedData-method split,RangedData-method [,RangedData,ANY,ANY,ANY-method [<-,RangedData,ANY,ANY,ANY-method [[,RangedData-method [[<-,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
Keywords: utilities
Description: RangedData utility functions
URL: ../../../library/IRanges/html/RangedData-utils.html

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

Entry: Ranges-class
Aliases: class:Ranges Ranges-class Ranges length,Ranges-method width start,Ranges-method width,Ranges-method end,Ranges-method start<- width<- end<- isEmpty isEmpty,Ranges-method as.matrix,Ranges-method as.data.frame,Ranges-method duplicated,Ranges-method show,Ranges-method [<-,Ranges,ANY,ANY,ANY-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: RangesList-class
Aliases: RangesList-class RangesList end,RangesList-method isEmpty,RangesList-method width,RangesList-method start,RangesList-method as.data.frame,RangesList-method coerce,RangesList,IRangesList-method show,RangesList-method summary,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
Keywords: utilities
Description: RangesList utility functions
URL: ../../../library/IRanges/html/RangesList-utils.html

Entry: RangesMatching-class
Aliases: RangesMatching-class matchMatrix matchMatrix,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: Sequence-class
Aliases: class:Sequence Sequence-class Sequence class:SequenceORvector SequenceORvector-class SequenceORvector subseq subseq,SequenceORvector-method rep,Sequence-method [<-,Sequence,ANY,ANY,ANY-method !=,Sequence,Sequence-method class:XSequence XSequence-class XSequence length,XSequence-method subseq,XSequence-method coerce,integer,XSequence-method coerce,numeric,XSequence-method class:XRaw XRaw-class XRaw class:XInteger XInteger-class XInteger as.integer,XInteger-method as.vector,XInteger,missing-method coerce,integer,XInteger-method [,XInteger,ANY,ANY,ANY-method show,XInteger-method ==,XInteger,XInteger-method class:XNumeric XNumeric-class XNumeric as.numeric,XNumeric-method as.vector,XNumeric,missing-method coerce,numeric,XNumeric-method [,XNumeric,ANY,ANY,ANY-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,ANY,ANY,ANY-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: SplitXDataFrame-class
Aliases: SplitXDataFrame-class dim,SplitXDataFrame-method dimnames,SplitXDataFrame-method SplitXDataFrame as.data.frame,SplitXDataFrame-method unlist,SplitXDataFrame-method coerce,SplitXDataFrame,XDataFrame-method
Keywords: methods classes
Description: Split XDataFrame
URL: ../../../library/IRanges/html/SplitXDataFrame-class.html

Entry: TypedList-class
Aliases: TypedList-class elementClass elementClass,TypedList-method elements elements,TypedList-method length,TypedList-method names,TypedList-method names<-,TypedList-method [,TypedList,ANY,ANY,ANY-method [<-,TypedList,ANY,ANY,ANY-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,function-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 width<-,Views-method newViews Views views [[,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
Keywords: methods
Description: Views objects
URL: ../../../library/IRanges/html/Views-class.html

Entry: Views-utils
Aliases: Views-utils slice slice,integer-method slice,XInteger-method slice,XRleInteger-method viewMins viewMins,XIntegerViews-method viewMins,XRleIntegerViews-method viewMaxs viewMaxs,XIntegerViews-method viewMaxs,XRleIntegerViews-method viewSums viewSums,XIntegerViews-method viewSums,XRleIntegerViews-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,ANY-method XDataFrame [,XDataFrame,ANY,ANY,ANY-method [[,XDataFrame-method [[<-,XDataFrame-method as.data.frame,XDataFrame-method coerce,ANY,XDataFrame-method coerce,matrix,XDataFrame-method coerce,integer,XDataFrame-method coerce,data.frame,XDataFrame-method coerce,XDataFrame,data.frame-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: 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 as.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 as.integer,XRleIntegerViews-method
Keywords: methods classes
Description: The XRleIntegerViews class
URL: ../../../library/IRanges/html/XRleIntegerViews-class.html

Entry: coverage
Aliases: coverage coverage,IRanges-method coverage,MaskCollection-method
Keywords: methods
Description: Coverage across a set of ranges
URL: ../../../library/IRanges/html/coverage.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

Entry: solveUserSEW
Aliases: solveUserSEW
Keywords: utilities
Description: The SEW (Start/End/Width) interface
URL: ../../../library/IRanges/html/solveUserSEW.html
