mariner-package	mariner-package
$,MatrixSelection-method	MatrixSelection
+,MatrixSelection,MatrixSelection-method	MatrixSelection
-,MatrixSelection,MatrixSelection-method	MatrixSelection
adjustEnrichment	adjustEnrichment
adjustEnrichment,DelayedMatrix_OR_matrix,GInteractions-method	adjustEnrichment
aggHicMatrices	aggHicMatrices
aggHicMatrices,InteractionArray-method	aggHicMatrices
aggPairMcols	aggPairMcols
aggPairMcols,MergedGInteractions,character,character_OR_function_OR_list-method	aggPairMcols
as_ginteractions	as_ginteractions
as_ginteractions,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method	as_ginteractions
binPairs	binPairs
binPairs,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method	binPairs
binPairs,GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method	binPairs
binRanges	binRanges
binRanges,GRanges,numeric,character_OR_numeric_OR_missing-method	binRanges
calcLoopEnrichment	calcLoopEnrichment
calcLoopEnrichment,GInteractions,character-method	calcLoopEnrichment
cbind,InteractionArray-method	InteractionArray-class
cbind,InteractionMatrix-method	InteractionMatrix-class
changePixelRes	changePixelRes
changePixelRes,GInteractions,character-method	changePixelRes
CountMatrix	CountMatrix-class
CountMatrix-class	CountMatrix-class
counts,InteractionArray-method	counts
counts,InteractionMatrix-method	counts
counts<-,InteractionMatrix-method	counts
DelegatingGInteractions-class	DelegatingGInteractions-class
end1	GInteractions-accessors
end1,GInteractions_OR_InteractionSet-method	GInteractions-accessors
end2	GInteractions-accessors
end2,GInteractions_OR_InteractionSet-method	GInteractions-accessors
getPairClusters	getPairClusters
getPairClusters,MergedGInteractions-method	getPairClusters
hdf5BlockApply	hdf5BlockApply
hdf5BlockApply,DelayedArray-method	hdf5BlockApply
initialize,DelegatingGInteractions-method	initialize-DelegatingGInteractions-method
initialize,MergedGInteractions-method	initialize-MergedGInteractions-method
InteractionArray	InteractionArray-class
InteractionArray,ANY,GInteractions-method	InteractionArray-class
InteractionArray,missing,missing-method	InteractionArray-class
InteractionArray-class	InteractionArray-class
InteractionMatrix	InteractionMatrix-class
InteractionMatrix,ANY,GInteractions-method	InteractionMatrix-class
InteractionMatrix,missing,missing-method	InteractionMatrix-class
InteractionMatrix-class	InteractionMatrix-class
makeGInteractionsFromDataFrame	as_ginteractions
makeGInteractionsFromDataFrame,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method	as_ginteractions
mariner	mariner-package
MatrixSelection	MatrixSelection-class
MatrixSelection-class	MatrixSelection-class
MergedGInteractions	MergedGInteractions-class
MergedGInteractions-class	MergedGInteractions-class
mergePairs	mergePairs
mergePairs,list_OR_SimpleList_OR_GInteractions,numeric-method	mergePairs
names.MatrixSelection	MatrixSelection
parallel_slot_names,MergedGInteractions-method	parallel_slot_names-MergedGInteractions-method
path,InteractionMatrix-method	path
path<-,InteractionMatrix-method	path
pixelsToMatrices	pixelsToMatrices
pixelsToMatrices,GInteractions,numeric-method	pixelsToMatrices
plotEnrichment	adjustEnrichment
plotEnrichment,numeric,GInteractions-method	adjustEnrichment
plotMatrix	plotMatrix
plotMatrix,DelayedMatrix_OR_matrix-method	plotMatrix
pullHicMatrices	pullHicMatrices
pullHicMatrices,GInteractions,character,numeric-method	pullHicMatrices
pullHicPixels	pullHicPixels
pullHicPixels,GInteractions,character,numeric-method	pullHicPixels
rbind,InteractionArray-method	InteractionArray-class
rbind,InteractionMatrix-method	InteractionMatrix-class
removeShortPairs	removeShortPairs
removeShortPairs,GInteractions-method	removeShortPairs
selectBlock	selection-functions
selectBlock,numeric-method	selection-functions
selectBottomLeft	selection-functions
selectBottomLeft,numeric-method	selection-functions
selectBottomRight	selection-functions
selectBottomRight,numeric-method	selection-functions
selectCenterPixel	selection-functions
selectCenterPixel,numeric-method	selection-functions
selectCols	selection-functions
selectCols,numeric-method	selection-functions
selectCoordinates	selection-functions
selectCoordinates,numeric-method	selection-functions
selectCorners	selection-functions
selectCorners,numeric-method	selection-functions
selectInner	selection-functions
selectInner,numeric-method	selection-functions
selectionMethod	selectionMethod
selectionMethod,MergedGInteractions-method	selectionMethod
selectOuter	selection-functions
selectOuter,numeric-method	selection-functions
selectPixel	selectPixel
selectPixel,InteractionArray-method	selectPixel
selectRadius	selection-functions
selectRadius,numeric-method	selection-functions
selectRows	selection-functions
selectRows,numeric-method	selection-functions
selectSubmatrix	selection-functions
selectSubmatrix,matrix-method	selection-functions
selectTopLeft	selection-functions
selectTopLeft,numeric-method	selection-functions
selectTopRight	selection-functions
selectTopRight,numeric-method	selection-functions
seqnames1	GInteractions-accessors
seqnames1,GInteractions_OR_InteractionSet-method	GInteractions-accessors
seqnames2	GInteractions-accessors
seqnames2,GInteractions_OR_InteractionSet-method	GInteractions-accessors
shiftRanges	shiftRanges
shiftRanges,GRanges,character_OR_numeric-method	shiftRanges
show,CountMatrix-method	CountMatrix-class
show,InteractionArray-method	InteractionArray-class
show,InteractionMatrix-method	InteractionMatrix-class
show,MatrixSelection-method	selection-functions
snapToBins	snapToBins
snapToBins,GInteractions,numeric-method	snapToBins
snapToBins,GRanges,numeric-method	snapToBins
sources	sources
sources,MergedGInteractions-method	sources
start1	GInteractions-accessors
start1,GInteractions_OR_InteractionSet-method	GInteractions-accessors
start2	GInteractions-accessors
start2,GInteractions_OR_InteractionSet-method	GInteractions-accessors
subsetBySource	subsetBySource
subsetBySource,MergedGInteractions,character_OR_missing,character_OR_missing-method	subsetBySource
subsetBySource,MergedGInteractions,character_OR_missing,missing-method	subsetBySource
subsetBySource,MergedGInteractions,missing,character_OR_missing-method	subsetBySource
subsetBySource,MergedGInteractions,missing,missing-method	subsetBySource
[[,MatrixSelection,ANY,ANY-method	MatrixSelection
