IRanges
Foundation of integer range manipulation in Bioconductor

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1313
Source code
81
Man pages
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IRanges: Foundation of integer range manipulation in Bioconductor
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API

API for IRanges
Foundation of integer range manipulation in Bioconductor

Global functions
!,CompressedList-method Man page
%outside% Man page
%over% Man page
%within% Man page
.IPosRanges_as_integer_pairs Source code
.IPosRanges_summary Source code
.IPos_summary Source code
.IRanges.reverse Source code
.NCList_xp Source code
.append.names.or.desc Source code
.as.data.frame.IPos Source code
.as.data.frame.IPosRanges Source code
.as.list.CompressedNormalIRangesList Source code
.as.list.SortedByQueryHits Source code
.asNormalIRanges Source code
.check_IntegerRanges_for_coercion_to_IPos Source code
.check_arg_names Source code
.check_start_or_end_or_width Source code
.check_that_Views_objects_are_concatenable Source code
.concatenate_CompressedList_objects Source code
.concatenate_StitchedIPos_objects Source code
.concatenate_Views_objects Source code
.coverage_IRanges Source code
.default_countOverlaps Source code
.dotargsAsList Source code
.duplicated.CompressedAtomicList Source code
.duplicated.CompressedList Source code
.duplicated.Dups Source code
.extractListFragments_by_Partitioning Source code
.extractPartitioningFragments_by_Partitioning Source code
.extract_groups_from_RangesList Source code
.fold_and_truncate_coverage Source code
.from_Hits_to_CompressedIntegerList Source code
.from_IPosRanges_to_CompressedIntegerList Source code
.from_IPosRanges_to_naked_character_matrix_for_display Source code
.from_IPos_to_naked_character_matrix_for_display Source code
.from_IntegerRangesList_to_SimpleNormalIRangesList Source code
.from_IntegerRanges_to_CompressedIPosList Source code
.from_IntegerRanges_to_CompressedIRangesList Source code
.from_IntegerRanges_to_StitchedIPos Source code
.from_IntegerRanges_to_UnstitchedIPos Source code
.from_List_to_CompressedIRangesList Source code
.from_List_to_SimpleIRangesList Source code
.from_SortedByQueryHits_to_CompressedIntegerList Source code
.from_SortedByQueryHits_to_PartitioningByEnd Source code
.from_StitchedIPos_to_UnstitchedIPos Source code
.from_UnstitchedIPos_to_StitchedIPos Source code
.from_character_to_IRanges Source code
.from_factor_to_IRanges Source code
.from_integer_to_IRanges Source code
.from_list_to_CompressedIRangesList Source code
.from_list_to_SimpleIRangesList Source code
.from_logical_to_NormalIRanges Source code
.gaps_CompressedIRangesList Source code
.gaps_RangesList Source code
.guessGapFileCOL2CLASS Source code
.isNormal_IRanges Source code
.make_PartitioningByEnd_from_aranges Source code
.make_StitchedIPos_from_pos Source code
.make_UnstitchedIPos_from_pos_runs Source code
.max_CompressedNormalIRangesList Source code
.merge_IntegerRangesList Source code
.min_CompressedNormalIRangesList Source code
.nclist Source code
.nclists Source code
.newEmptyMask Source code
.newH2LGrouping Source code
.normargSEW Source code
.normargSEW0 Source code
.normarg_circle.length1 Source code
.normarg_circle.length2 Source code
.normarg_n Source code
.normarg_nchunk_or_chunksize Source code
.normarg_pos Source code
.normarg_shift Source code
.normarg_shift_or_weight_list Source code
.normarg_stitch Source code
.normarg_totalsize Source code
.numeric2end Source code
.numeric2width Source code
.onUnload Source code
.order_IPosRanges Source code
.prepare_Partitioning_names Source code
.range_CompressedIRangesList Source code
.read.agpORgapFile Source code
.read.agpORgapMask Source code
.read.liftFile Source code
.read.rmFile Source code
.read.trfFile Source code
.reconcile_mcols Source code
.reduce_CompressedIRangesList Source code
.restrict_IntegerRanges Source code
.setAtomicListMethod Source code
.setListMethod Source code
.set_IRanges_end Source code
.set_IRanges_start Source code
.set_IRanges_width Source code
.set_Views_ranges Source code
.shift_ranges_in_groups_to_first_circle Source code
.shift_ranges_to_first_circle Source code
.showAtomicList Source code
.showDistinctSeqnamesAndStop Source code
.splitAsList_by_Rle Source code
.splitAsList_by_factor Source code
.splitAsList_by_integer Source code
.splitAsList_by_integer_Rle Source code
.split_and_remap_hits Source code
.subset_by_integer Source code
.summaryRleViewsList Source code
.tapplyDefault Source code
.test Source code
.unique.CompressedList Source code
.unique.RleList Source code
.unlist_width Source code
.unsafe_new_StitchedIPos Source code
.unsafe_new_UnstitchedIPos Source code
.updateObject_IPos Source code
.valid.CompressedList Source code
.valid.CompressedList.partitioning Source code
.valid.CompressedList.unlistData Source code
.valid.H2LGrouping Source code
.valid.MaskCollection Source code
.valid.MaskCollection.active Source code
.valid.MaskCollection.desc Source code
.valid.MaskCollection.names Source code
.valid.MaskCollection.nir_list Source code
.valid.MaskCollection.width Source code
.valid.NormalIRanges Source code
.valid.NormalIRangesList Source code
.valid.PartitioningByEnd Source code
.valid.PartitioningByWidth Source code
.valid.PartitioningMap Source code
.valid.SimpleSplitDataFrameList Source code
.validate_IPos Source code
AtomicList Man page
AtomicList-class Man page
AtomicList-utils Man page
AtomicListConstructor Source code
CharacterList Man page
CharacterList-class Man page
CoercerToList Source code
Complex,CompressedAtomicList-method Man page
Complex,SimpleAtomicList-method Man page
ComplexList Man page
ComplexList-class Man page
CompressedAtomicList Man page
CompressedAtomicList-class Man page
CompressedCharacterList Man page
CompressedCharacterList-class Man page
CompressedComplexList Man page
CompressedComplexList-class Man page
CompressedDFrameList Man page
CompressedDFrameList-class Man page
CompressedDataFrameList Man page
CompressedDataFrameList-class Man page
CompressedFactorList Man page
CompressedFactorList-class Man page
CompressedGrouping-class Man page
CompressedHitsList Man page Source code
CompressedHitsList-class Man page
CompressedIRangesList Man page
CompressedIRangesList-class Man page
CompressedIntegerList Man page
CompressedIntegerList-class Man page
CompressedList Man page
CompressedList-class Man page
CompressedLogicalList Man page
CompressedLogicalList-class Man page
CompressedManyToManyGrouping-class Man page
CompressedManyToOneGrouping-class Man page
CompressedNormalIRangesList Man page
CompressedNormalIRangesList-class Man page
CompressedNumericList Man page
CompressedNumericList-class Man page
CompressedRawList Man page
CompressedRawList-class Man page
CompressedRleList Man page
CompressedRleList-class Man page
CompressedSplitDFrameList Man page
CompressedSplitDFrameList-class Man page
CompressedSplitDataFrameList Man page
CompressedSplitDataFrameList-class Man page
DFrameList Man page
DFrameList-class Man page
DataFrameList Man page Source code
DataFrameList-class Man page
Dups Man page Source code
Dups-class Man page
FactorList Man page
FactorList-class Man page
Grouping Man page
Grouping-class Man page
GroupingIRanges Man page
GroupingIRanges-class Man page
GroupingRanges Man page
GroupingRanges-class Man page
H2LGrouping Man page Source code
H2LGrouping-class Man page
Hits-examples Man page
INCOMPATIBLE_ARANGES_MSG Man page
IPos Man page Source code
IPos-class Man page
IPosRanges Man page
IPosRanges-class Man page
IPosRanges-comparison Man page
IQR,AtomicList-method Man page
IRanges Man page Source code
IRanges-class Man page
IRanges-constructor Man page
IRanges-utils Man page
IRangesList Man page Source code
IRangesList-class Man page
IntegerList Man page
IntegerList-class Man page
IntegerRanges Man page
IntegerRanges-class Man page
IntegerRangesList Man page
IntegerRangesList-class Man page
IntegerRanges_OR_missing Man page
IntegerRanges_OR_missing-class Man page
LogicalList Man page
LogicalList-class Man page
ManyToManyGrouping Man page Source code
ManyToManyGrouping-class Man page
ManyToOneGrouping Man page Source code
ManyToOneGrouping-class Man page
Mask Man page Source code
MaskCollection Man page
MaskCollection-class Man page
MaskCollection.show_frame Man page Source code
Math,CompressedAtomicList-method Man page
Math,SimpleAtomicList-method Man page
Math2,CompressedAtomicList-method Man page
Math2,SimpleAtomicList-method Man page
NCList Man page Source code
NCList-class Man page
NCLists Man page Source code
NCLists-class Man page
NROW,DataFrameList-method Man page
NormalIRanges Man page
NormalIRanges-class Man page
NormalIRangesList Man page
NormalIRangesList-class Man page
NumericList Man page
NumericList-class Man page
Ops,AtomicList,atomic-method Man page
Ops,CompressedAtomicList,CompressedAtomicList-method Man page
Ops,CompressedAtomicList,SimpleAtomicList-method Man page
Ops,CompressedAtomicList,atomic-method Man page
Ops,CompressedRangesList,numeric-method Man page
Ops,Ranges,numeric-method Man page
Ops,RangesList,numeric-method Man page
Ops,SimpleAtomicList,CompressedAtomicList-method Man page
Ops,SimpleAtomicList,SimpleAtomicList-method Man page
Ops,SimpleAtomicList,atomic-method Man page
Ops,atomic,AtomicList-method Man page
Ops,atomic,CompressedAtomicList-method Man page
Ops,atomic,SimpleAtomicList-method Man page
Partitioning Man page
Partitioning-class Man page
PartitioningByEnd Man page Source code
PartitioningByEnd-class Man page
PartitioningByWidth Man page Source code
PartitioningByWidth-class Man page
PartitioningMap Man page Source code
PartitioningMap-class Man page
ROWNAMES,DataFrameList-method Man page
RangedSelection Man page Source code
RangedSelection-class Man page
RangesList Source code
RawList Man page
RawList-class Man page
RleList Man page
RleList,AtomicList,RleList-method Man page
RleList-class Man page
RleViews Man page
RleViews-class Man page
RleViews.show_vframe Source code
RleViews.show_vframe_header Source code
RleViews.show_vframe_line Source code
RleViewsList Man page Source code
RleViewsList-class Man page
SimpleAtomicList Man page
SimpleAtomicList-class Man page
SimpleCharacterList Man page
SimpleCharacterList-class Man page
SimpleComplexList Man page
SimpleComplexList-class Man page
SimpleDFrameList Man page
SimpleDFrameList-class Man page
SimpleDataFrameList Man page
SimpleDataFrameList-class Man page
SimpleFactorList Man page
SimpleFactorList-class Man page
SimpleGrouping-class Man page
SimpleIRangesList Man page
SimpleIRangesList-class Man page
SimpleIntegerList Man page
SimpleIntegerList-class Man page
SimpleIntegerRangesList Man page
SimpleIntegerRangesList-class Man page
SimpleLogicalList Man page
SimpleLogicalList-class Man page
SimpleManyToManyGrouping-class Man page
SimpleManyToOneGrouping-class Man page
SimpleNormalIRangesList Man page
SimpleNormalIRangesList-class Man page
SimpleNumericList Man page
SimpleNumericList-class Man page
SimpleRawList Man page
SimpleRawList-class Man page
SimpleRleList Man page
SimpleRleList-class Man page
SimpleRleViewsList-class Man page
SimpleSplitDFrameList Man page
SimpleSplitDFrameList-class Man page
SimpleSplitDataFrameList Man page
SimpleSplitDataFrameList-class Man page
SimpleViewsList Man page
SimpleViewsList-class Man page
SplitDFrameList Man page
SplitDFrameList-class Man page
SplitDataFrameList Man page Source code
SplitDataFrameList-class Man page
StitchedIPos Man page
StitchedIPos-class Man page
Summary,AtomicList-method Man page
Summary,CompressedRleList-method Man page
Summary,Views-method Man page
UnstitchedIPos Man page
UnstitchedIPos-class Man page
Views Man page
Views,Rle-method Man page
Views,RleList-method Man page
Views-class Man page
ViewsList Man page
ViewsList-class Man page
[,CompressedSplitDataFrameList-method Man page
[,SimpleSplitDataFrameList-method Man page
[<-,SplitDataFrameList-method Man page
[[,SDFLWrapperForTransform-method Man page
[[<-,SDFLWrapperForTransform-method Man page
`%outside%` Source code
`%over%` Source code
`%poutside%` Source code
`%pover%` Source code
`%pwithin%` Source code
`%within%` Source code
`.window<-.Vector` Source code
`splitAsList<-` Source code
`window<-.Vector` Source code
`window<-.factor` Source code
active Man page
active,MaskCollection-method Man page
active<- Man page
active<-,MaskCollection-method Man page
all,CompressedAtomicList-method Man page
all,CompressedRleList-method Man page
any,CompressedAtomicList-method Man page
anyNA,CompressedAtomicList-method Man page
append,MaskCollection,MaskCollection-method Man page
as.character,IPosRanges-method Man page
as.data.frame,IPos-method Man page
as.data.frame,IPosRanges-method Man page
as.data.frame.IPos Man page Source code
as.data.frame.IPosRanges Man page Source code
as.env,SDFLWrapperForTransform-method Man page
as.factor,IPosRanges-method Man page
as.factor2 Source code
as.list,CompressedAtomicList-method Man page
as.list,CompressedNormalIRangesList-method Man page
as.list,Hits-method Man page
as.list,SortedByQueryHits-method Man page
as.matrix,AtomicList-method Man page
as.matrix,CompressedHitsList-method Man page
as.matrix,IPosRanges-method Man page
as.matrix,Views-method Man page
as.matrix,ViewsList-method Man page
as.matrix.AtomicList Source code
as.vector,AtomicList-method Man page
asNormalIRanges Man page Source code
as_list_of_IRanges Source code
bindROWS,CompressedList-method Man page
bindROWS,IPos-method Man page
bindROWS,NCList-method Man page
bindROWS,Partitioning-method Man page
bindROWS,Views-method Man page
breakInChunks Man page Source code
cbind,DataFrameList-method Man page
centeredIRanges Source code
chartr,ANY,ANY,CompressedCharacterList-method Man page
chartr,ANY,ANY,CompressedRleList-method Man page
chartr,ANY,ANY,SimpleCharacterList-method Man page
chartr,ANY,ANY,SimpleRleList-method Man page
class:AtomicList Man page
class:CharacterList Man page
class:ComplexList Man page
class:CompressedAtomicList Man page
class:CompressedCharacterList Man page
class:CompressedComplexList Man page
class:CompressedDFrameList Man page
class:CompressedDataFrameList Man page
class:CompressedFactorList Man page
class:CompressedGrouping Man page
class:CompressedHitsList Man page
class:CompressedIRangesList Man page
class:CompressedIntegerList Man page
class:CompressedList Man page
class:CompressedLogicalList Man page
class:CompressedManyToManyGrouping Man page
class:CompressedManyToOneGrouping Man page
class:CompressedNormalIRangesList Man page
class:CompressedNumericList Man page
class:CompressedRawList Man page
class:CompressedRleList Man page
class:CompressedSplitDFrameList Man page
class:CompressedSplitDataFrameList Man page
class:DFrameList Man page
class:DataFrameList Man page
class:Dups Man page
class:FactorList Man page
class:Grouping Man page
class:GroupingIRanges Man page
class:GroupingRanges Man page
class:H2LGrouping Man page
class:IPos Man page
class:IPosRanges Man page
class:IRanges Man page
class:IRangesList Man page
class:IntegerList Man page
class:IntegerRanges Man page
class:IntegerRangesList Man page
class:IntegerRanges_OR_missing Man page
class:LogicalList Man page
class:ManyToManyGrouping Man page
class:ManyToOneGrouping Man page
class:MaskCollection Man page
class:NCList Man page
class:NCLists Man page
class:NormalIRanges Man page
class:NormalIRangesList Man page
class:NumericList Man page
class:Partitioning Man page
class:PartitioningByEnd Man page
class:PartitioningByWidth Man page
class:PartitioningMap Man page
class:RawList Man page
class:RleList Man page
class:RleViews Man page
class:SimpleAtomicList Man page
class:SimpleCharacterList Man page
class:SimpleComplexList Man page
class:SimpleDFrameList Man page
class:SimpleDataFrameList Man page
class:SimpleFactorList Man page
class:SimpleGrouping Man page
class:SimpleIRangesList Man page
class:SimpleIntegerList Man page
class:SimpleIntegerRangesList Man page
class:SimpleLogicalList Man page
class:SimpleManyToManyGrouping Man page
class:SimpleManyToOneGrouping Man page
class:SimpleNormalIRangesList Man page
class:SimpleNumericList Man page
class:SimpleRawList Man page
class:SimpleRleList Man page
class:SimpleSplitDFrameList Man page
class:SimpleSplitDataFrameList Man page
class:SimpleViewsList Man page
class:SplitDFrameList Man page
class:SplitDataFrameList Man page
class:StitchedIPos Man page
class:UnstitchedIPos Man page
class:Views Man page
class:ViewsList Man page
classNameForDisplay,CompressedDFrameList-method Man page
classNameForDisplay,CompressedList-method Man page
classNameForDisplay,SimpleDFrameList-method Man page
coerce,ANY,CompressedDataFrameList-method Man page
coerce,ANY,CompressedList-method Man page
coerce,ANY,CompressedSplitDFrameList-method Man page
coerce,ANY,CompressedSplitDataFrameList-method Man page
coerce,ANY,DataFrameList-method Man page
coerce,ANY,IPos-method Man page
coerce,ANY,IntegerRanges-method Man page
coerce,ANY,SimpleDataFrameList-method Man page
coerce,ANY,SimpleSplitDFrameList-method Man page
coerce,ANY,SimpleSplitDataFrameList-method Man page
coerce,ANY,SplitDFrameList-method Man page
coerce,ANY,SplitDataFrameList-method Man page
coerce,ANY,StitchedIPos-method Man page
coerce,ANY,UnstitchedIPos-method Man page
coerce,ANY,vector-method Man page
coerce,AtomicList,CharacterList-method Man page
coerce,AtomicList,ComplexList-method Man page
coerce,AtomicList,IntegerList-method Man page
coerce,AtomicList,LogicalList-method Man page
coerce,AtomicList,NumericList-method Man page
coerce,AtomicList,RawList-method Man page
coerce,AtomicList,RleList-method Man page
coerce,AtomicList,RleViews Man page
coerce,CompressedAtomicList,list-method Man page
coerce,CompressedIRangesList,CompressedNormalIRangesList-method Man page
coerce,CompressedRleList,CompressedIRangesList-method Man page
coerce,DataFrame,Grouping-method Man page
coerce,DataFrame,SplitDFrameList-method Man page
coerce,DataFrameList,DFrame-method Man page
coerce,FactorList,Grouping-method Man page
coerce,Hits,CompressedIntegerList-method Man page
coerce,Hits,Grouping Man page
coerce,Hits,Grouping-method Man page
coerce,Hits,IntegerList-method Man page
coerce,Hits,List-method Man page
coerce,IRanges,NormalIRanges-method Man page
coerce,IntegerRanges,CompressedIRangesList-method Man page
coerce,IntegerRanges,IPos-method Man page
coerce,IntegerRanges,IRanges-method Man page
coerce,IntegerRanges,NCList-method Man page
coerce,IntegerRanges,PartitioningByEnd-method Man page
coerce,IntegerRanges,PartitioningByWidth-method Man page
coerce,IntegerRanges,StitchedIPos-method Man page
coerce,IntegerRanges,UnstitchedIPos-method Man page
coerce,IntegerRangesList,CompressedNormalIRangesList-method Man page
coerce,IntegerRangesList,NCLists-method Man page
coerce,IntegerRangesList,NormalIRangesList-method Man page
coerce,IntegerRangesList,RangedSelection-method Man page
coerce,IntegerRangesList,SimpleIRangesList-method Man page
coerce,IntegerRangesList,SimpleNormalIRangesList-method Man page
coerce,List,CompressedIRangesList-method Man page
coerce,List,CompressedSplitDFrameList-method Man page
coerce,List,IRangesList-method Man page
coerce,List,SimpleIRangesList-method Man page
coerce,List,SimpleSplitDFrameList-method Man page
coerce,LogicalList,CompressedNormalIRangesList-method Man page
coerce,LogicalList,NormalIRangesList-method Man page
coerce,LogicalList,SimpleNormalIRangesList-method Man page
coerce,ManyToOneGrouping,factor-method Man page
coerce,MaskCollection,NormalIRanges-method Man page
coerce,NCLists,CompressedIRangesList-method Man page
coerce,NCLists,IRangesList-method Man page
coerce,NormalIRangesList,CompressedNormalIRangesList-method Man page
coerce,Rle,IRanges-method Man page
coerce,Rle,NormalIRanges-method Man page
coerce,RleList,CompressedNormalIRangesList-method Man page
coerce,RleList,NormalIRangesList-method Man page
coerce,RleList,SimpleNormalIRangesList-method Man page
coerce,RleViewsList,IRangesList-method Man page
coerce,RleViewsList,SimpleIRangesList-method Man page
coerce,SimpleIRangesList,SimpleNormalIRangesList-method Man page
coerce,SimpleIntegerRangesList,SimpleIRangesList-method Man page
coerce,SimpleList,SimpleIRangesList-method Man page
coerce,SimpleList,SplitDFrameList-method Man page
coerce,SortedByQueryHits,CompressedIntegerList-method Man page
coerce,SortedByQueryHits,IRanges-method Man page
coerce,SortedByQueryHits,IntegerList-method Man page
coerce,SortedByQueryHits,IntegerRanges-method Man page
coerce,SortedByQueryHits,List-method Man page
coerce,SortedByQueryHits,Partitioning-method Man page
coerce,SortedByQueryHits,PartitioningByEnd-method Man page
coerce,SplitDataFrameList,DFrame-method Man page
coerce,StitchedIPos,UnstitchedIPos-method Man page
coerce,UnstitchedIPos,StitchedIPos-method Man page
coerce,Vector,Views-method Man page
coerce,Views,IRanges-method Man page
coerce,Views,IntegerRanges-method Man page
coerce,Views,NormalIRanges-method Man page
coerce,character,IRanges-method Man page
coerce,factor,IRanges-method Man page
coerce,grouping,Grouping-method Man page
coerce,grouping,ManyToOneGrouping-method Man page
coerce,integer,IRanges-method Man page
coerce,integer,NormalIRanges-method Man page
coerce,list,CompressedIRangesList-method Man page
coerce,list,IRangesList-method Man page
coerce,list,SimpleIRangesList-method Man page
coerce,list,SplitDFrameList-method Man page Man page
coerce,logical,IRanges-method Man page
coerce,logical,NormalIRanges-method Man page
coerce,numeric,IRanges-method Man page
coerce,numeric,NormalIRanges-method Man page
coerce,vector,AtomicList-method Man page
coerce,vector,CompressedCharacterList-method Man page
coerce,vector,CompressedComplexList-method Man page
coerce,vector,CompressedIntegerList-method Man page
coerce,vector,CompressedLogicalList-method Man page
coerce,vector,CompressedNumericList-method Man page
coerce,vector,CompressedRawList-method Man page
coerce,vector,CompressedRleList-method Man page
coerce,vector,Grouping-method Man page
coerce,vector,ManyToManyGrouping-method Man page
coerce,vector,ManyToOneGrouping-method Man page
coerce,vector,SimpleCharacterList-method Man page
coerce,vector,SimpleComplexList-method Man page
coerce,vector,SimpleIntegerList-method Man page
coerce,vector,SimpleLogicalList-method Man page
coerce,vector,SimpleNumericList-method Man page
coerce,vector,SimpleRawList-method Man page
coerce,vector,SimpleRleList-method Man page
coerceToCompressedList Source code
collapse Man page
collapse,MaskCollection-method Man page
colnames,CompressedSplitDataFrameList-method Man page
colnames,DataFrameList-method Man page
colnames,RangedSelection-method Man page
colnames,SDFLWrapperForTransform-method Man page
colnames,SplitDataFrameList-method Man page
colnames<-,CompressedSplitDataFrameList-method Man page
colnames<-,RangedSelection-method Man page
colnames<-,SimpleDataFrameList-method Man page
columnMetadata Man page
columnMetadata,CompressedSplitDataFrameList-method Man page
columnMetadata,SimpleSplitDataFrameList-method Man page
columnMetadata<- Man page
columnMetadata<-,CompressedSplitDataFrameList-method Man page
columnMetadata<-,SimpleSplitDataFrameList-method Man page
cor,AtomicList,AtomicList-method Man page
countOverlaps Man page
countOverlaps,IntegerRanges,IntegerRanges-method Man page
countOverlaps,IntegerRangesList,IntegerRangesList-method Man page
countOverlaps,Vector,Vector-method Man page
countOverlaps,Vector,missing-method Man page
countOverlaps,integer,Vector-method Man page
countOverlaps_IntegerRanges Source code
cov,AtomicList,AtomicList-method Man page
coverage Man page
coverage,IntegerRanges-method Man page
coverage,IntegerRangesList-method Man page
coverage,StitchedIPos-method Man page
coverage,Views-method Man page
coverage-methods Man page
coverage_CompressedIRangesList Source code
cummax,CompressedAtomicList-method Man page
cummin,CompressedAtomicList-method Man page
cumprod,CompressedAtomicList-method Man page
cumsum,CompressedAtomicList-method Man page
cvg_IntegerRanges Source code
cvg_IntegerRangesList Source code
default_overlapsAny Source code
default_splitAsList Source code
default_subsetByOverlaps Source code
desc Man page
desc,MaskCollection-method Man page
desc<- Man page
desc<-,MaskCollection-method Man page
diceRangesByList Source code
diff,CompressedAtomicList-method Man page
diff.AtomicList Man page Source code
dim,DataFrameList-method Man page
dimnames,DataFrameList-method Man page
dimnames<-,DataFrameList-method Man page
disjoin Man page
disjoin,CompressedIRangesList-method Man page
disjoin,IntegerRanges-method Man page
disjoin,IntegerRangesList-method Man page
disjoin,NormalIRanges-method Man page
disjointBins Man page
disjointBins,IntegerRanges-method Man page
disjointBins,IntegerRangesList-method Man page
disjointBins,NormalIRanges-method Man page
distance Man page
distance,IntegerRanges,IntegerRanges-method Man page
distance,Pairs,missing-method Man page
distanceToNearest Man page
distanceToNearest,IntegerRanges,IntegerRanges_OR_missing-method Man page
doBinaryCompressedListOp Source code
drop,AtomicList-method Man page
duplicated,CompressedAtomicList-method Man page
duplicated,CompressedList-method Man page
duplicated,Dups-method Man page
effective_restriction_window_for_IntegerRanges Source code
effective_restriction_windows_for_IntegerRangesList Source code
elementNROWS,CompressedList-method Man page
elementNROWS,NCLists-method Man page
elementNROWS,Ranges-method Man page
emptyOpsReturnValue Source code
end,CompressedRangesList-method Man page
end,NCList-method Man page
end,NCLists-method Man page
end,PartitioningByEnd-method Man page
end,PartitioningByWidth-method Man page
end,Pos-method Man page
end,Ranges-method Man page
end,RangesList-method Man page
end,SimpleViewsList-method Man page
end<- Man page
end<-,IRanges-method Man page
end<-,IntegerRangesList-method Man page
end<-,Views-method Man page
equisplit Man page Source code
eval Man page
eval,expression,Vector-method Man page
eval,language,Vector-method Man page
extractList Man page
extractList,ANY,ANY-method Man page
extractList,ANY-method Man page
extractListFragments Man page Source code
extractROWS,IPos-method Man page
extractROWS,NCList,ANY-method Man page
extractROWS,Partitioning-method Man page
extract_pos_runs_by_ranges Source code
findOverlapPairs Man page Source code
findOverlaps Man page
findOverlaps,ANY,Pairs-method Man page
findOverlaps,IntegerRanges,IntegerRanges-method Man page
findOverlaps,IntegerRangesList,IntegerRangesList-method Man page
findOverlaps,Pairs,ANY-method Man page
findOverlaps,Pairs,Pairs-method Man page
findOverlaps,Pairs,missing-method Man page
findOverlaps,Vector,missing-method Man page
findOverlaps,integer,IntegerRanges-method Man page
findOverlaps-methods Man page
findOverlaps_IntegerRanges Source code
findOverlaps_IntegerRanges_Partitioning Source code
findOverlaps_NCList Source code
findOverlaps_NCLists Source code
findRange Man page
findRange,Rle-method Man page
find_overlaps_in_groups_NCList Source code
flank Man page
flank,Ranges-method Man page
flank,RangesList-method Man page
follow Man page
follow,IntegerRanges,IntegerRanges_OR_missing-method Man page
from,CompressedHitsList-method Man page
gaps Man page
gaps,CompressedIRangesList-method Man page
gaps,IntegerRanges-method Man page
gaps,IntegerRangesList-method Man page
gaps,MaskCollection-method Man page
gaps,Views-method Man page
getListElement,IPosRanges-method Man page
get_IPos_version Source code
global2local_revmap Source code
grouplengths Man page
grouplengths,CompressedGrouping-method Man page
grouplengths,Grouping-method Man page
grouplengths,GroupingRanges-method Man page
grouplengths,H2LGrouping-method Man page
grouprank Man page
grouprank,H2LGrouping-method Man page
gsub,ANY,ANY,CompressedCharacterList-method Man page
gsub,ANY,ANY,CompressedRleList-method Man page
gsub,ANY,ANY,SimpleCharacterList-method Man page
gsub,ANY,ANY,SimpleRleList-method Man page
heads Source code
high2low Man page
high2low,ANY-method Man page
high2low,H2LGrouping-method Man page
ifelse2 Man page
ifelse2,ANY,ANY,List-method Man page
ifelse2,ANY,List,ANY-method Man page
ifelse2,CompressedLogicalList,ANY,ANY-method Man page
ifelse2,CompressedLogicalList,ANY,List-method Man page
ifelse2,CompressedLogicalList,List,ANY-method Man page Man page
ifelse2,CompressedLogicalList,List,List-method Man page
ifelse2,List,ANY,ANY-method Man page
ifelse2,SimpleLogicalList,ANY,ANY-method Man page
ifelse2,SimpleLogicalList,ANY,List-method Man page
ifelse2,SimpleLogicalList,List,ANY-method Man page Man page
ifelse2,SimpleLogicalList,List,List-method Man page
ifelseReturnValue Source code
inter-range-methods Man page
interaction2 Source code
intersect Man page
intersect,CompressedAtomicList,CompressedAtomicList-method Man page
intersect,CompressedIRangesList,CompressedIRangesList-method Man page
intersect,IntegerRanges,IntegerRanges-method Man page
intersect,IntegerRangesList,IntegerRangesList-method Man page
intersect,Pairs,missing-method Man page
intra-range-methods Man page
is.na,CompressedList-method Man page
is.unsorted,IPosRanges-method Man page
isDisjoint Man page
isDisjoint,IntegerRanges-method Man page
isDisjoint,IntegerRangesList-method Man page
isDisjoint,NormalIRanges-method Man page
isDisjoint,StitchedIPos-method Man page
isEmpty,NormalIRanges-method Man page
isEmpty,Ranges-method Man page
isNormal Man page
isNormal,CompressedIRangesList-method Man page
isNormal,IRanges-method Man page
isNormal,IntegerRangesList-method Man page
isNormal,NormalIRanges-method Man page
isNormal,Ranges-method Man page
isNormal,SimpleIRangesList-method Man page
lapply,CompressedAtomicList-method Man page
lapply,CompressedList-method Man page
lapply_CompressedList Source code
length,CompressedList-method Man page
length,H2LGrouping-method Man page
length,IPos-method Man page
length,MaskCollection-method Man page
length,NCList-method Man page
length,NCLists-method Man page
length,PartitioningByEnd-method Man page
length,PartitioningByWidth-method Man page
length,Ranges-method Man page
length,UnstitchedIPos-method Man page
length<-,H2LGrouping-method Man page
levelCols Source code
local2global_revmap Source code
low2high Man page
low2high,H2LGrouping-method Man page
mad,AtomicList-method Man page
makeGroupNames Source code
make_IRanges_from_windows_args Source code
mapOrder Man page
mapOrder,PartitioningMap-method Man page
maskedratio Man page
maskedratio,MaskCollection-method Man page
maskedwidth Man page
maskedwidth,MaskCollection-method Man page
match,CompressedList,vector-method Man page
match,IPosRanges,IPosRanges-method Man page
max,CompressedNormalIRangesList-method Man page
max,MaskCollection-method Man page
max,NormalIRanges-method Man page
max,SimpleNormalIRangesList-method Man page
max,Views-method Man page
mean,AtomicList-method Man page
mean,CompressedIntegerList-method Man page
mean,CompressedLogicalList-method Man page
mean,CompressedNumericList-method Man page
mean,CompressedRleList-method Man page
mean,Views-method Man page
median,AtomicList-method Man page
median,CompressedAtomicList-method Man page
members Man page
members,H2LGrouping-method Man page
members,ManyToOneGrouping-method Man page
merge,IntegerRangesList,IntegerRangesList-method Man page
merge,IntegerRangesList,missing-method Man page
merge,missing,IntegerRangesList-method Man page
mergeByOverlaps Man page Source code
mid Man page
mid,Ranges-method Man page
min,CompressedNormalIRangesList-method Man page
min,MaskCollection-method Man page
min,NormalIRanges-method Man page
min,SimpleNormalIRangesList-method Man page
min,Views-method Man page
multisplit Man page Source code
nLnode,CompressedHitsList-method Man page
nRnode,CompressedHitsList-method Man page
names,CompressedList-method Man page
names,IPos-method Man page
names,IRanges-method Man page
names,MaskCollection-method Man page
names,NCList-method Man page
names,NCLists-method Man page
names,Partitioning-method Man page
names,Views-method Man page
names<-,CompressedList-method Man page
names<-,IPos-method Man page
names<-,IRanges-method Man page
names<-,MaskCollection-method Man page
names<-,Partitioning-method Man page
names<-,Views-method Man page
narrow Man page
narrow,ANY-method Man page
narrow,MaskCollection-method Man page
nchar,CompressedCharacterList-method Man page
nchar,CompressedRleList-method Man page
nchar,SimpleCharacterList-method Man page
nchar,SimpleRleList-method Man page
nchar_CompressedList Source code
ncol,CompressedSplitDataFrameList-method Man page
ncol,DataFrameList-method Man page
ncol,SimpleSplitDataFrameList-method Man page
nearest Man page
nearest,IntegerRanges,IntegerRanges_OR_missing-method Man page
nearest-methods Man page
newCompressedList0 Source code
newNormalIRangesFromIRanges Source code
new_CompressedList_from_list Source code
new_StitchedIPos Source code
new_UnstitchedIPos Source code
new_Views Source code
nir_list Man page
nir_list,MaskCollection-method Man page
nobj Man page
nobj,BaseManyToManyGrouping-method Man page
nobj,CompressedManyToOneGrouping-method Man page
nobj,H2LGrouping-method Man page
nobj,ManyToManyGrouping-method Man page
nobj,ManyToOneGrouping-method Man page
nobj,PartitioningByEnd-method Man page
normSplitFactor Source code
nrow,DataFrameList-method Man page
order,CompressedAtomicList-method Man page
order,IPosRanges-method Man page
order,List-method Man page
overlapsAny Man page
overlapsAny,IntegerRangesList,IntegerRangesList-method Man page
overlapsAny,Vector,Vector-method Man page
overlapsAny,Vector,missing-method Man page
overlapsAny,integer,Vector-method Man page
overlapsRanges Man page
overlapsRanges,IntegerRanges,IntegerRanges-method Man page
overlapsRanges,IntegerRangesList,IntegerRangesList-method Man page
parallel_slot_names,IPos-method Man page
parallel_slot_names,IRanges-method Man page
parallel_slot_names,NCLists-method Man page
parallel_slot_names,Partitioning-method Man page
parallel_slot_names,PartitioningByEnd-method Man page
parallel_slot_names,PartitioningByWidth-method Man page
parallel_slot_names,UnstitchedIPos-method Man page
parallel_slot_names,Views-method Man page
paste,CompressedAtomicList-method Man page
pcompare Man page
pcompare,IPosRanges,IPosRanges-method Man page
pgap Man page
pgap,IntegerRanges,IntegerRanges-method Man page
pintersect Man page
pintersect,IntegerRanges,IntegerRanges-method Man page
pintersect,Pairs,missing-method Man page
pmax,IntegerList-method Man page
pmax,NumericList-method Man page
pmax,RleList-method Man page
pmax.int,IntegerList-method Man page
pmax.int,NumericList-method Man page
pmax.int,RleList-method Man page
pmin,IntegerList-method Man page
pmin,NumericList-method Man page
pmin,RleList-method Man page
pmin.int,IntegerList-method Man page
pmin.int,NumericList-method Man page
pmin.int,RleList-method Man page
pos Man page
pos,CompressedPosList-method Man page
pos,IPos-method Man page
pos,PosList-method Man page
pos,UnstitchedIPos-method Man page
poverlaps Man page
poverlaps,IntegerRanges,IntegerRanges-method Man page
poverlaps,IntegerRanges,integer-method Man page
poverlaps,integer,IntegerRanges-method Man page
precede Man page
precede,IntegerRanges,IntegerRanges_OR_missing-method Man page
print_NCList Source code
promoters Man page
promoters,IntegerRanges-method Man page
promoters,RangesList-method Man page
psetdiff Man page
psetdiff,IntegerRanges,IntegerRanges-method Man page
psetdiff,Pairs,missing-method Man page
punion Man page
punion,IntegerRanges,IntegerRanges-method Man page
punion,Pairs,missing-method Man page
quantile,AtomicList-method Man page
range Man page
range,CompressedIRangesList-method Man page
range,CompressedIntegerList-method Man page
range,CompressedLogicalList-method Man page
range,CompressedNumericList-method Man page
range,IntegerRanges-method Man page
range,IntegerRangesList-method Man page
range,StitchedIPos-method Man page
range-squeezers Man page
rangeComparisonCodeToLetter Man page Source code
ranges Man page
ranges,CompressedRleList-method Man page
ranges,IntegerRanges-method Man page
ranges,NCLists-method Man page
ranges,RangedSelection-method Man page
ranges,Rle-method Man page
ranges,RleList-method Man page
ranges,SimpleViewsList-method Man page
ranges,Views-method Man page
ranges<- Man page
ranges<-,RangedSelection-method Man page
ranges<-,Views-method Man page
rank,CompressedAtomicList-method Man page
rank,List-method Man page
rbind,DataFrameList-method Man page
read.Mask Man page
read.agpMask Man page Source code
read.gapMask Man page Source code
read.liftMask Man page Source code
read.rmMask Man page Source code
read.trfMask Man page Source code
recycleList Source code
recycleListElements Source code
reduce Man page
reduce,CompressedIRangesList-method Man page
reduce,IntegerRanges-method Man page
reduce,IntegerRangesList-method Man page
reduce,Views-method Man page
reflect Man page
reflect,IntegerRanges-method Man page
regroup Man page Source code
regroupBySupergroup Source code
relist Man page
relist,ANY,List-method Man page
relist,ANY,PartitioningByEnd-method Man page Man page
relist,Vector,list-method Man page
repLengthOneElements Source code
replace_with_mcol_if_single_string Source code
resize Man page
resize,Ranges-method Man page
resize,RangesList-method Man page
resplit Source code
restrict Man page
restrict,IntegerRanges-method Man page
restrict,RangesList-method Man page
restrict,Views-method Man page
revElements,CompressedList-method Man page
reverse Man page
reverse,IRanges-method Man page
reverse,MaskCollection-method Man page
reverse,NormalIRanges-method Man page
reverse,Views-method Man page
reverse,character-method Man page
rglist Man page
rglist,Pairs-method Man page
rownames,DataFrameList-method Man page
rownames<-,CompressedSplitDataFrameList-method Man page
rownames<-,SimpleDataFrameList-method Man page
rowsumCompressedList Source code
runLength,CompressedRleList-method Man page
runLength,RleList-method Man page
runValue,CompressedRleList-method Man page
runValue,RleList-method Man page
runValue<-,CompressedRleList-method Man page
runValue<-,SimpleRleList-method Man page
runmean,RleList-method Man page
runmed,CompressedIntegerList-method Man page
runmed,NumericList-method Man page
runmed,RleList-method Man page
runmed,SimpleIntegerList-method Man page
runq,RleList-method Man page
runsum,RleList-method Man page
runwtsum,RleList-method Man page
sd,AtomicList-method Man page
selectNearest Man page Source code
selfmatch,CompressedAtomicList-method Man page
selfmatch,IPosRanges-method Man page
setCompressedListSummaryMethod Source code
setCompressedListWhichSummaryMethod Source code
setCompressedNumericalListMethod Source code
setListCoercions Source code
set_IRanges_names Source code
setdiff Man page
setdiff,CompressedIRangesList,CompressedIRangesList-method Man page
setdiff,IntegerRanges,IntegerRanges-method Man page
setdiff,IntegerRangesList,IntegerRangesList-method Man page
setdiff,Pairs,missing-method Man page
setops-methods Man page
shift Man page
shift,IPos-method Man page
shift,Ranges-method Man page
shift,RangesList-method Man page
show,AtomicList-method Man page
show,Dups-method Man page
show,Grouping-method Man page
show,IPos-method Man page
show,IPosRanges-method Man page
show,IntegerRangesList-method Man page
show,MaskCollection-method Man page
show,PartitioningMap-method Man page
show,RleList-method Man page
show,RleViews-method Man page
show,SplitDataFrameList-method Man page
show_IPos Source code
show_IPosRanges Source code
show_IntegerRangesList Source code
slice Man page
slice,ANY-method Man page
slice,Rle-method Man page
slice,RleList-method Man page
slice-methods Man page
slidingIRanges Source code
slidingViews Source code
slidingWindows Man page
slidingWindows,IPosRanges-method Man page
smoothEnds,CompressedIntegerList-method Man page
smoothEnds,NumericList-method Man page
smoothEnds,RleList-method Man page
smoothEnds,SimpleIntegerList-method Man page
solveUserSEW Man page Source code
solveUserSEW0 Man page Source code
solveUserSEWForSingleSeq Source code
sort,List-method Man page
space Man page
space,CompressedHitsList-method Man page
space,IntegerRangesList-method Man page
split<-,Vector-method Man page
splitRanges Man page
splitRanges,Rle-method Man page
splitRanges,vector_OR_factor-method Man page
stack,DataFrameList-method Man page
start,CompressedRangesList-method Man page
start,IRanges-method Man page
start,NCList-method Man page
start,NCLists-method Man page
start,PartitioningByEnd-method Man page
start,PartitioningByWidth-method Man page
start,Pos-method Man page
start,Ranges-method Man page
start,RangesList-method Man page
start,SimpleViewsList-method Man page
start,Views-method Man page
start<- Man page
start<-,IRanges-method Man page
start<-,IntegerRangesList-method Man page
start<-,Views-method Man page
stitch_IntegerRanges Source code
sub,ANY,ANY,CompressedCharacterList-method Man page
sub,ANY,ANY,CompressedRleList-method Man page
sub,ANY,ANY,SimpleCharacterList-method Man page
sub,ANY,ANY,SimpleRleList-method Man page
subgrouping Source code
subject Man page
subject,SimpleRleViewsList-method Man page
subject,Views-method Man page
subsetByOverlaps Man page
subsetByOverlaps,Vector,Vector-method Man page
subviews Man page
subviews,Views-method Man page
successiveIRanges Man page Source code
successiveViews Man page Source code
sum,CompressedIntegerList-method Man page
sum,CompressedLogicalList-method Man page
sum,CompressedNumericList-method Man page
sum,Views-method Man page
summary,CompressedIRangesList-method Man page
summary,IPos-method Man page
summary,IPosRanges-method Man page
summary.IPos Man page Source code
summary.IPosRanges Man page Source code
table,AtomicList-method Man page
table,SimpleAtomicList-method Man page
tails Source code
tapply,ANY,Vector-method Man page
tapply,Vector,ANY-method Man page
tapply,Vector,Vector-method Man page
threebands Man page
threebands,IRanges-method Man page
tile Man page
tile,IPosRanges-method Man page
to,CompressedHitsList-method Man page
toFactor Source code
toglobal Source code
togroup Man page
togroup,ANY-method Man page
togroup,H2LGrouping-method Man page
togroup,ManyToOneGrouping-method Man page
togroup,Partitioning-method Man page
togrouplength Man page
togrouplength,ManyToOneGrouping-method Man page
togrouprank Man page
togrouprank,H2LGrouping-method Man page
tolower,CompressedCharacterList-method Man page
tolower,CompressedRleList-method Man page
tolower,SimpleCharacterList-method Man page
tolower,SimpleRleList-method Man page
toupper,CompressedCharacterList-method Man page
toupper,CompressedRleList-method Man page
toupper,SimpleCharacterList-method Man page
toupper,SimpleRleList-method Man page
transform,SplitDataFrameList-method Man page
transform.SplitDataFrameList Source code
trim Man page
trim,Views-method Man page
union Man page
union,CompressedIRangesList,CompressedIRangesList-method Man page
union,IntegerRanges,IntegerRanges-method Man page
union,IntegerRangesList,IntegerRangesList-method Man page
union,Pairs,missing-method Man page
unique,CompressedList-method Man page
unique,RleList-method Man page
unlist,CompressedList-method Man page
unlist,SimpleFactorList-method Man page
unlist,SimpleNormalIRangesList-method Man page
unlist,SimpleRleList-method Man page
unlist,Views-method Man page
unlist_as_integer Source code
unsplit,List-method Man page
unstrsplit,CharacterList-method Man page
unstrsplit,RleList-method Man page
updateObject,IPos-method Man page
update_ranges Man page
update_ranges,IRanges-method Man page
update_ranges,Views-method Man page
validate_Pos Source code
validate_Ranges Source code
var,AtomicList,AtomicList-method Man page
var,AtomicList,missing-method Man page
vectorToHits Source code
view-summarization-methods Man page
viewApply Man page
viewApply,RleViews-method Man page
viewApply,RleViewsList-method Man page
viewApply,Views-method Man page
viewMaxs Man page
viewMaxs,RleViews-method Man page
viewMaxs,RleViewsList-method Man page
viewMeans Man page
viewMeans,RleViews-method Man page
viewMeans,RleViewsList-method Man page
viewMins Man page
viewMins,RleViews-method Man page
viewMins,RleViewsList-method Man page
viewRangeMaxs Man page
viewRangeMaxs,RleViews-method Man page
viewRangeMaxs,RleViewsList-method Man page
viewRangeMins Man page
viewRangeMins,RleViews-method Man page
viewRangeMins,RleViewsList-method Man page
viewSums Man page
viewSums,RleViews-method Man page
viewSums,RleViewsList-method Man page
viewWhichMaxs Man page
viewWhichMaxs,RleViews-method Man page
viewWhichMaxs,RleViewsList-method Man page
viewWhichMins Man page
viewWhichMins,RleViews-method Man page
viewWhichMins,RleViewsList-method Man page
vmembers Man page
vmembers,H2LGrouping-method Man page
vmembers,ManyToOneGrouping-method Man page
which,CompressedLogicalList-method Man page
which,CompressedRleList-method Man page
which,SimpleLogicalList-method Man page
which,SimpleRleList-method Man page
which.max,CompressedRleList-method Man page
which.max,IntegerList-method Man page
which.max,NumericList-method Man page
which.max,RleList-method Man page
which.max,Views-method Man page
which.min,CompressedRleList-method Man page
which.min,IntegerList-method Man page
which.min,NumericList-method Man page
which.min,RleList-method Man page
which.min,Views-method Man page
whichAsIRanges Man page Source code
whichFirstNotNormal Man page
whichFirstNotNormal,IntegerRangesList-method Man page
whichFirstNotNormal,Ranges-method Man page
width Man page
width,CompressedRangesList-method Man page
width,IRanges-method Man page
width,MaskCollection-method Man page
width,NCList-method Man page
width,NCLists-method Man page
width,PartitioningByEnd-method Man page
width,PartitioningByWidth-method Man page
width,Pos-method Man page
width,Ranges-method Man page
width,RangesList-method Man page
width,SimpleViewsList-method Man page
width,Views-method Man page
width<- Man page
width<-,IRanges-method Man page
width<-,IntegerRangesList-method Man page
width<-,Views-method Man page
window<-,Vector-method Man page
window<-,factor-method Man page
window<-,vector-method Man page
window<-.Vector Man page
window<-.factor Man page
window<-.vector Man page
windows,Ranges-method Man page
with,Vector-method Man page
IRanges documentation built on Dec. 14, 2020, 2 a.m.

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