API for Bioconductor/IRanges
Infrastructure for manipulating intervals on sequences

Global functions
!,CompressedList-method Man page
$<-,CompressedList-method Man page
$<-,RangedData-method Man page
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
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
CompressedIRangesList.coverage Source code
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
CompressedNormalIRangesList.max Source code
CompressedNormalIRangesList.min Source code
CompressedNumericList Man page
CompressedNumericList-class Man page
CompressedRawList Man page
CompressedRawList-class Man page
CompressedRleList Man page
CompressedRleList-class Man page
CompressedSplitDataFrameList-class Man page
DataFrame-utils 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
IPos Man page Source code
IPos-class Man page
IQR,AtomicList-method Man page
IRanges Man page Source code
IRanges-class Man page
IRanges-constructor Man page
IRanges-utils Man page
IRanges.coverage Source code
IRanges.reverse Source code
IRangesList Man page Source code
IRangesList-class Man page
IntegerList Man page
IntegerList-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
NCList_find_overlaps_in_groups Source code
NCList_xp Source code
NCLists Man page Source code
NCLists-class 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,CompressedIRangesList,numeric-method Man page
Ops,Ranges,ANY-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
RangedData Man page Source code
RangedData-class Man page
RangedData_fromDataFrame Source code
RangedSelection Man page Source code
RangedSelection-class Man page
Ranges Man page
Ranges-class Man page
Ranges-comparison Man page
Ranges.restrict Source code
RangesList Man page Source code
RangesList-class Man page
RangesList.merge Source code
RangesORmissing Man page
RangesORmissing-class Man page
Ranges_as_IntegerPairs 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
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
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
SimpleRangesList Man page
SimpleRangesList-class Man page
SimpleRawList Man page
SimpleRawList-class Man page
SimpleRleList Man page
SimpleRleList-class Man page
SimpleRleViewsList-class Man page
SimpleSplitDataFrameList-class Man page
SimpleViewsList Man page
SimpleViewsList-class Man page
SplitDataFrameList Man page Source code
SplitDataFrameList-class Man page
Summary,AtomicList-method Man page
Summary,CompressedRleList-method Man page
Summary,Views-method 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
[,RangedData-method Man page
[,SimpleSplitDataFrameList-method Man page
[<-,SplitDataFrameList-method Man page
[[,RangedData-method Man page
[[,SDFLWrapperForTransform-method Man page
[[<-,CompressedList-method Man page
[[<-,RangedData-method Man page
[[<-,SDFLWrapperForTransform-method Man page
\%outside\% Man page
\%over\% Man page
\%within\% Man page
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
append.names.or.desc Source code
as.character,Ranges-method Man page
as.data.frame,Hits-method Man page
as.data.frame,IPos-method Man page
as.data.frame,RangedData-method Man page
as.data.frame,Ranges-method Man page
as.data.frame.DataFrameList Source code
as.data.frame.Hits Source code
as.data.frame.RangedData Source code
as.data.frame.Ranges Source code
as.data.frame.RangesList Source code
as.env,RangedData-method Man page
as.env,SDFLWrapperForTransform-method Man page
as.factor,Ranges-method Man page
as.factor2 Source code
as.integer,Ranges-method Man page
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.list.CompressedNormalIRangesList Source code
as.list.SortedByQueryHits Source code
as.matrix,AtomicList-method Man page
as.matrix,CompressedHitsList-method Man page
as.matrix,Ranges-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 Source code
as_list_of_IRanges Source code
bindROWS Source code
breakInChunks Man page Source code
c,CompressedList-method Man page
c,IPos-method Man page
c,IRanges-method Man page
c,RangedData-method Man page
c,Views-method Man page
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
check_arg_names Source code
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: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: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:IRanges Man page
class:IRangesList Man page
class:IntegerList 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:RangedData Man page
class:Ranges Man page
class:RangesList-class Man page
class:RangesORmissing 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:SimpleFactorList Man page
class:SimpleGrouping Man page
class:SimpleIRangesList Man page
class:SimpleIntegerList Man page
class:SimpleLogicalList Man page
class:SimpleManyToManyGrouping Man page
class:SimpleManyToOneGrouping Man page
class:SimpleNormalIRangesList Man page
class:SimpleNumericList Man page
class:SimpleRangesList-class Man page
class:SimpleRawList Man page
class:SimpleRleList Man page
class:SimpleViewsList Man page
class:Views Man page
class:ViewsList Man page
classNameForDisplay,CompressedList-method Man page
coerce,ANY,CompressedList-method Man page
coerce,ANY,CompressedSplitDataFrameList-method Man page
coerce,ANY,IPos-method Man page
coerce,ANY,Ranges-method Man page
coerce,ANY,SimpleSplitDataFrameList-method Man page
coerce,ANY,SplitDataFrameList-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,SplitDataFrameList-method Man page
coerce,DataFrameList,DataFrame-method Man page
coerce,DataTable,RangedData-method Man page
coerce,FactorList,Grouping-method Man page
coerce,Hits,CompressedIntegerList-method Man page
coerce,Hits,DataFrame-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,List,CompressedIRangesList-method Man page
coerce,List,CompressedSplitDataFrameList-method Man page
coerce,List,IRangesList-method Man page
coerce,List,SimpleIRangesList-method Man page
coerce,List,SimpleSplitDataFrameList-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,RangedData,CompressedIRangesList-method Man page
coerce,RangedData,DataFrame-method Man page
coerce,RangedData,IRangesList-method Man page
coerce,RangedData,RangesList-method Man page
coerce,Ranges,CompressedIRangesList-method Man page
coerce,Ranges,IPos-method Man page
coerce,Ranges,IRanges-method Man page
coerce,Ranges,NCList-method Man page
coerce,Ranges,PartitioningByEnd-method Man page
coerce,Ranges,PartitioningByWidth-method Man page
coerce,Ranges,RangedData-method Man page
coerce,Ranges,RangesList-method Man page
coerce,RangesList,CompressedNormalIRangesList-method Man page
coerce,RangesList,NCLists-method Man page
coerce,RangesList,NormalIRangesList-method Man page
coerce,RangesList,RangedData-method Man page
coerce,RangesList,RangedSelection-method Man page
coerce,RangesList,SimpleIRangesList-method Man page
coerce,RangesList,SimpleNormalIRangesList-method Man page
coerce,RangesList,SimpleRangesList-method Man page
coerce,Rle,IRanges-method Man page
coerce,Rle,NormalIRanges-method Man page
coerce,Rle,RangedData-method Man page
coerce,RleList,CompressedNormalIRangesList-method Man page
coerce,RleList,NormalIRangesList-method Man page
coerce,RleList,RangedData-method Man page
coerce,RleList,SimpleNormalIRangesList-method Man page
coerce,RleViewsList,CompressedIRangesList-method Man page
coerce,RleViewsList,IRangesList-method Man page
coerce,RleViewsList,RangedData-method Man page
coerce,RleViewsList,SimpleIRangesList-method Man page
coerce,SimpleIRangesList,SimpleNormalIRangesList-method Man page
coerce,SimpleList,SplitDataFrameList-method Man page
coerce,SimpleRangesList,SimpleIRangesList-method Man page
coerce,SortedByQueryHits,CompressedIntegerList-method Man page
coerce,SortedByQueryHits,IRanges-method Man page
coerce,SortedByQueryHits,IntegerList-method Man page
coerce,SortedByQueryHits,List-method Man page
coerce,SortedByQueryHits,Partitioning-method Man page
coerce,SortedByQueryHits,PartitioningByEnd-method Man page
coerce,SortedByQueryHits,Ranges-method Man page
coerce,SplitDataFrameList,DataFrame-method Man page
coerce,Vector,Views-method Man page
coerce,Views,IRanges-method Man page
coerce,Views,NormalIRanges-method Man page
coerce,Views,Ranges-method Man page
coerce,character,IRanges-method Man page
coerce,data.frame,RangedData-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,RangesList-method Man page
coerce,list,SimpleIRangesList-method Man page
coerce,list,SplitDataFrameList-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,RangedData-method Man page
colnames,RangedSelection-method Man page
colnames,SimpleSplitDataFrameList-method Man page
colnames<-,CompressedSplitDataFrameList-method Man page
colnames<-,RangedData-method Man page
colnames<-,RangedSelection-method Man page
colnames<-,SimpleDataFrameList-method Man page
columnMetadata Man page
columnMetadata,CompressedSplitDataFrameList-method Man page
columnMetadata,RangedData-method Man page
columnMetadata,SimpleSplitDataFrameList-method Man page
columnMetadata<- Man page
columnMetadata<-,CompressedSplitDataFrameList-method Man page
columnMetadata<-,RangedData-method Man page
columnMetadata<-,SimpleSplitDataFrameList-method Man page
combine_CompressedList_objects Source code
combine_IPos_objects Source code
compress_listData Source code
cor,AtomicList,AtomicList-method Man page
countOverlaps Man page
countOverlaps,RangedData,RangedData-method Man page
countOverlaps,RangedData,RangesList-method Man page
countOverlaps,Ranges,Ranges-method Man page
countOverlaps,RangesList,RangedData-method Man page
countOverlaps,RangesList,RangesList-method Man page
countOverlaps,Vector,Vector-method Man page
countOverlaps,Vector,ViewsList-method Man page
countOverlaps,Vector,missing-method Man page
countOverlaps,ViewsList,Vector-method Man page
countOverlaps,ViewsList,ViewsList-method Man page
countOverlaps_Ranges Source code
countOverlaps_default Source code
cov,AtomicList,AtomicList-method Man page
coverage Man page
coverage,RangedData-method Man page
coverage,Ranges-method Man page
coverage,RangesList-method Man page
coverage,Views-method Man page
coverage-methods Man page
cummax,CompressedAtomicList-method Man page
cummin,CompressedAtomicList-method Man page
cumprod,CompressedAtomicList-method Man page
cumsum,CompressedAtomicList-method Man page
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,NormalIRanges-method Man page
disjoin,Ranges-method Man page
disjoin,RangesList-method Man page
disjointBins Man page
disjointBins,NormalIRanges-method Man page
disjointBins,Ranges-method Man page
disjointBins,RangesList-method Man page
distance Man page
distance,Pairs,missing-method Man page
distance,Ranges,Ranges-method Man page
distanceToNearest Man page
distanceToNearest,Ranges,RangesORmissing-method Man page
doBinaryCompressedListOp Source code
dotargsAsList Source code
drop,AtomicList-method Man page
duplicated,CompressedAtomicList-method Man page
duplicated,CompressedList-method Man page
duplicated,Dups-method Man page
duplicated.CompressedAtomicList Source code
duplicated.CompressedList Source code
duplicated.Dups Source code
elementNROWS,CompressedList-method Man page
elementNROWS,NCLists-method Man page
elementNROWS,RangedData-method Man page
elementNROWS,Ranges-method Man page
elementNROWS,Views-method Man page
emptyOpsReturnValue Source code
end,CompressedIRangesList-method Man page
end,IPos-method Man page
end,NCList-method Man page
end,NCLists-method Man page
end,PartitioningByEnd-method Man page
end,PartitioningByWidth-method Man page
end,RangedData-method Man page
end,Ranges-method Man page
end,RangesList-method Man page
end,SimpleViewsList-method Man page
end,Views-method Man page
end<- Man page
end<-,IRanges-method Man page
end<-,RangedData-method Man page
end<-,RangesList-method Man page
end<-,Views-method Man page
endoapply,CompressedList-method Man page
endoapply,RangedData-method Man page
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
extractROWS,IPos-method Man page
extract_groups_from_RangesList Source code
extract_pos_runs_by_ranges Source code
findOverlapPairs Man page Source code
findOverlaps Man page
findOverlaps,ANY,Pairs-method Man page
findOverlaps,Pairs,ANY-method Man page
findOverlaps,Pairs,Pairs-method Man page
findOverlaps,Pairs,missing-method Man page
findOverlaps,RangedData,RangedData-method Man page
findOverlaps,RangedData,RangesList-method Man page
findOverlaps,Ranges,Ranges-method Man page
findOverlaps,RangesList,RangedData-method Man page
findOverlaps,RangesList,RangesList-method Man page
findOverlaps,Vector,Views-method Man page
findOverlaps,Vector,ViewsList-method Man page
findOverlaps,Vector,missing-method Man page
findOverlaps,Views,Vector-method Man page
findOverlaps,Views,Views-method Man page
findOverlaps,ViewsList,Vector-method Man page
findOverlaps,ViewsList,ViewsList-method Man page
findOverlaps,integer,Ranges-method Man page
findOverlaps-methods Man page
findOverlaps_NCList Source code
findOverlaps_NCLists Source code
findOverlaps_Ranges Source code
findOverlaps_Ranges_Partitioning Source code
findRange Man page
findRange,Rle-method Man page
flank Man page
flank,CompressedIRangesList-method Man page
flank,Ranges-method Man page
flank,RangesList-method Man page
fold_and_truncate_coverage Source code
follow Man page
follow,Ranges,RangesORmissing-method Man page
from,CompressedHitsList-method Man page
fromRangedDataToCompressedIRangesList Source code
from_Hits_to_CompressedIntegerList Source code
from_List_to_CompressedIRangesList Source code
from_List_to_SimpleIRangesList Source code
from_RangesList_to_SimpleNormalIRangesList Source code
from_Ranges_to_CompressedIRangesList Source code
from_Ranges_to_IPos Source code
from_SortedByQueryHits_to_CompressedIntegerList Source code
from_SortedByQueryHits_to_PartitioningByEnd Source code
from_character_to_IRanges Source code
from_factor_to_IRanges Source code
from_list_to_CompressedIRangesList Source code
from_list_to_SimpleIRangesList Source code
gaps Man page
gaps,CompressedIRangesList-method Man page
gaps,MaskCollection-method Man page
gaps,Ranges-method Man page
gaps,RangesList-method Man page
gaps,Views-method Man page
gaps_CompressedIRangesList Source code
gaps_RangesList 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
guessGapFileCOL2CLASS 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,Pairs,missing-method Man page
intersect,Ranges,Ranges-method Man page
intersect,RangesList,RangesList-method Man page
intra-range-methods Man page
is.na,CompressedList-method Man page
is.unsorted,Ranges-method Man page
isDisjoint Man page
isDisjoint,IPos-method Man page
isDisjoint,NormalIRanges-method Man page
isDisjoint,Ranges-method Man page
isDisjoint,RangesList-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,NormalIRanges-method Man page
isNormal,Ranges-method Man page
isNormal,RangesList-method Man page
isNormal,SimpleIRangesList-method Man page
islistfactor Source code
lapply,CompressedAtomicList-method Man page
lapply,CompressedList-method Man page
lapply,RangedData-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,RangedData-method Man page
length,Ranges-method Man page
length,Views-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_naked_matrix_from_IPos Source code
make_naked_matrix_from_Ranges 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,Ranges,Ranges-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
mendoapply,CompressedList-method Man page
merge,RangesList,RangesList-method Man page
merge,RangesList,missing-method Man page
merge,missing,RangesList-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
mstack Man page
mstack,DataFrame-method Man page
mstack,Vector-method Man page
mstack,vector-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,RangedData-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<-,RangedData-method Man page
names<-,Views-method Man page
narrow Man page
narrow,CompressedIRangesList-method Man page
narrow,MaskCollection-method Man page
narrow,Ranges-method Man page
narrow,RangesList-method Man page
narrow,Views-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
nclist Source code
nclists Source code
ncol,CompressedSplitDataFrameList-method Man page
ncol,DataFrameList-method Man page
ncol,RangedData-method Man page
ncol,SimpleSplitDataFrameList-method Man page
nearest Man page
nearest,Ranges,RangesORmissing-method Man page
nearest-methods Man page
newCompressedList0 Source code
newEmptyMask Source code
newH2LGrouping Source code
newNormalIRangesFromIRanges Source code
new_CompressedList_from_list 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
normargAtomicList1 Source code
normargAtomicList2 Source code
normargSEW Source code
normargSEW0 Source code
normarg_chunksize_or_nchunk Source code
normarg_circle.length1 Source code
normarg_circle.length2 Source code
normarg_shift_or_weight Source code
normarg_totalsize Source code
nrow,DataFrameList-method Man page
nrow,RangedData-method Man page
numeric2end Source code
numeric2width Source code
onUnload Source code
order,CompressedAtomicList-method Man page
order,List-method Man page
order,Ranges-method Man page
order_Ranges Source code
overlapsAny Man page
overlapsAny,RangedData,RangedData-method Man page
overlapsAny,RangedData,RangesList-method Man page
overlapsAny,RangesList,RangedData-method Man page
overlapsAny,RangesList,RangesList-method Man page
overlapsAny,Vector,Vector-method Man page
overlapsAny,Vector,ViewsList-method Man page
overlapsAny,Vector,missing-method Man page
overlapsAny,ViewsList,Vector-method Man page
overlapsAny,ViewsList,ViewsList-method Man page
overlapsAny_default Source code
overlapsRanges Man page
overlapsRanges,Ranges,Ranges-method Man page
overlapsRanges,RangesList,RangesList-method Man page
paste,CompressedAtomicList-method Man page
pcompare Man page
pcompare,Ranges,Ranges-method Man page
pgap Man page
pgap,Ranges,Ranges-method Man page
pintersect Man page
pintersect,Pairs,missing-method Man page
pintersect,Ranges,Ranges-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,IPos-method Man page
poverlaps Man page
poverlaps,Ranges,Ranges-method Man page
poverlaps,Ranges,integer-method Man page
poverlaps,integer,Ranges-method Man page
precede Man page
precede,Ranges,RangesORmissing-method Man page
prepare_Partitioning_names Source code
print_NCList Source code
promoters Man page
promoters,CompressedIRangesList-method Man page
promoters,Ranges-method Man page
promoters,RangesList-method Man page
promoters,Views-method Man page
psetdiff Man page
psetdiff,Pairs,missing-method Man page
psetdiff,Ranges,Ranges-method Man page
punion Man page
punion,Pairs,missing-method Man page
punion,Ranges,Ranges-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,IPos-method Man page
range,RangedData-method Man page
range,Ranges-method Man page
range,RangesList-method Man page
range-squeezers Man page
rangeComparisonCodeToLetter Man page Source code
range_CompressedIRangesList Source code
ranges Man page
ranges,CompressedRleList-method Man page
ranges,Hits-method Man page
ranges,HitsList-method Man page
ranges,NCLists-method Man page
ranges,RangedData-method Man page
ranges,RangedSelection-method Man page
ranges,Ranges-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<-,RangedData-method 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
rbind,RangedData-method Man page
read.Mask Man page
read.agpMask Man page Source code
read.agpORgapFile Source code
read.agpORgapMask Source code
read.gapMask Man page Source code
read.liftFile Source code
read.liftMask Man page Source code
read.rmFile Source code
read.rmMask Man page Source code
read.trfFile Source code
read.trfMask Man page Source code
reconcileMetadatacols Source code
recycleList Source code
recycleListElements Source code
reduce Man page
reduce,CompressedIRangesList-method Man page
reduce,Ranges-method Man page
reduce,RangesList-method Man page
reduce,Views-method Man page
reduce_CompressedIRangesList Source code
reflect Man page
reflect,Ranges-method Man page
regroup Man page Source code
regroupBySupergroup Source code
relist,ANY,List-method Man page
relist,ANY,PartitioningByEnd-method Man page Man page
relist,Vector,list-method Man page
relistToClass,DataFrame-method Man page
relistToClass,data.frame-method Man page
rep,Vector-method Man page
rep.int,Vector-method Man page
repLengthOneElements Source code
resize Man page
resize,CompressedIRangesList-method Man page
resize,IntervalList-method Man page
resize,Ranges-method Man page
resize,RangesList-method Man page
resplit Source code
restrict Man page
restrict,CompressedIRangesList-method Man page
restrict,Ranges-method Man page
restrict,RangesList-method Man page
rev,Vector-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,RangedData-method Man page
rownames<-,CompressedSplitDataFrameList-method Man page
rownames<-,RangedData-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
sNormal_IRanges Source code
score,RangedData-method Man page
score<-,RangedData-method Man page
sd,AtomicList-method Man page
selectNearest Man page Source code
selfmatch,CompressedAtomicList-method Man page
selfmatch,Ranges-method Man page
setAtomicListMethod Source code
setCompressedListSummaryMethod Source code
setCompressedListWhichSummaryMethod Source code
setCompressedNumericalListMethod Source code
setListCoercions Source code
setListMethod Source code
set_IRanges_end Source code
set_IRanges_names Source code
set_IRanges_start Source code
set_IRanges_width Source code
set_Views_ranges Source code
setdiff Man page
setdiff,CompressedIRangesList,CompressedIRangesList-method Man page
setdiff,Pairs,missing-method Man page
setdiff,Ranges,Ranges-method Man page
setdiff,RangesList,RangesList-method Man page
setops-methods Man page
shift Man page
shift,CompressedIRangesList-method Man page
shift,IPos-method Man page
shift,Ranges-method Man page
shift,RangesList-method Man page
shift,Views-method Man page
shift_ranges_in_groups_to_first_circle Source code
shift_ranges_to_first_circle Source code
show,AtomicList-method Man page
show,Dups-method Man page
show,Grouping-method Man page
show,IPos-method Man page
show,MaskCollection-method Man page
show,PartitioningMap-method Man page
show,RangedData-method Man page
show,Ranges-method Man page
show,RangesList-method Man page
show,RleList-method Man page
show,RleViews-method Man page
show,SplitDataFrameList-method Man page
showAsCell,Ranges-method Man page
showAsCell,RangesList-method Man page
showAtomicList Source code
showDistinctSeqnamesAndStop Source code
showRanges Source code
showRangesList Source code
show_IPos 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,Ranges-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,RangedData-method Man page
space,RangesList-method Man page
split<-,Vector-method Man page
splitAsList Man page
splitAsList,ANY,ANY Man page
splitAsList_by_Rle Source code
splitAsList_by_factor Source code
splitAsList_by_integer Source code
splitAsList_by_integer_Rle Source code
splitAsList_default Source code
splitRanges Man page
splitRanges,Rle-method Man page
splitRanges,vector_OR_factor-method Man page
split_and_remap_hits Source code
stack,DataFrameList-method Man page
stack,List-method Man page
stack.ind Source code
start,CompressedIRangesList-method Man page
start,IPos-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,RangedData-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<-,RangedData-method Man page
start<-,RangesList-method Man page
start<-,Views-method Man page
stitch_IPos Source code
stitch_Ranges 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
subset,Vector-method Man page
subsetByOverlaps Man page
subsetByOverlaps,RangedData,RangedData-method Man page
subsetByOverlaps,RangedData,RangesList-method Man page
subsetByOverlaps,RangesList,RangedData-method Man page
subsetByOverlaps,Vector,Vector-method Man page
subset_by_integer Source code
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
summaryRleViewsList Source code
table,AtomicList-method Man page
table,SimpleAtomicList-method Man page
tapply,ANY,Vector-method Man page
tapply,Vector,ANY-method Man page
tapply,Vector,Vector-method Man page
tapplyDefault Source code
test Source code
threebands Man page
threebands,IRanges-method Man page
tile Man page
tile,Ranges-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,Pairs,missing-method Man page
union,Ranges,Ranges-method Man page
union,RangesList,RangesList-method Man page
unique,CompressedList-method Man page
unique,RleList-method Man page
unique.CompressedList Source code
unique.RleList Source code
universe Man page
universe,RangedData-method Man page
universe,RangesList-method Man page
universe,ViewsList-method Man page
universe<- Man page
universe<-,RangedData-method Man page
universe<-,RangesList-method Man page
universe<-,ViewsList-method Man page
unlist,CompressedList-method Man page
unlist,Ranges-method Man page
unlist,SimpleFactorList-method Man page
unlist,SimpleNormalIRangesList-method Man page
unlist,SimpleRleList-method Man page
unlist_width Source code
unsplit,List-method Man page
unstrsplit,CharacterList-method Man page
unstrsplit,RleList-method Man page
update,IRanges-method Man page
update,Ranges-method Man page
updateCompressedList Source code
update_IRanges 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.Partitioning Source code
valid.PartitioningByEnd Source code
valid.PartitioningByWidth Source code
valid.PartitioningMap Source code
valid.RangedData Source code
valid.RangedData.names Source code
valid.RangedData.ranges Source code
valid.Ranges Source code
valid.SplitDataFrameList Source code
valid.Views.width Source code
values,RangedData-method Man page
values<-,RangedData-method Man page
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,Ranges-method Man page
whichFirstNotNormal,RangesList-method Man page
width Man page
width,CompressedIRangesList-method Man page
width,IPos-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,RangedData-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<-,RangedData-method Man page
width<-,RangesList-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
with,Vector-method Man page
within,RangedData-method Man page
Bioconductor/IRanges documentation built on Sept. 22, 2017, 2:01 p.m.