Mariner: Explore the Hi-Cs

Documentation for package ‘mariner’ version 1.10.0

Help Pages

Mariner: Explore the Hi-Cs

-- A --

adjustEnrichment	Adjust loop enrichment to remove distance- dependent effect.
adjustEnrichment-method	Adjust loop enrichment to remove distance- dependent effect.
aggHicMatrices	Aggregate count matrices from InteractionArray objects
aggHicMatrices-method	Aggregate count matrices from InteractionArray objects
aggMetadata	Aggregate the metadata columns of merged pairs
aggMetadata-method	Aggregate the metadata columns of merged pairs
as.list-method	JaggedArray Class
assignToBins	Flexibly bin paired ranges
assignToBins-method	Flexibly bin paired ranges
as_ginteractions	Convert DataFrames to GInteraction objects
as_ginteractions-method	Convert DataFrames to GInteraction objects

-- B --

binRanges	Flexibly bin ranges
binRanges-method	Flexibly bin ranges

-- C --

calcLoopEnrichment	Calculate loop enrichment over background.
calcLoopEnrichment-method	Calculate loop enrichment over background.
cbind-method	InteractionArray Class
cbind-method	InteractionMatrix Class
changePixelRes	Change pixels from one resolution to another selecting the new pixel using Hi-C data.
changePixelRes-method	Change pixels from one resolution to another selecting the new pixel using Hi-C data.
clusters	Get clustered pairs from MergedGInteractions object
clusters-method	Get clustered pairs from MergedGInteractions object
colData-method	InteractionJaggedArray Class
countOverlaps	Overlap methods for InteractionJaggedArray
countOverlaps-method	Overlap methods for InteractionJaggedArray
counts-method	InteractionJaggedArray Class
counts-method	Access count matrices from InteractionArray or InteractionMatrix
counts<--method	Access count matrices from InteractionArray or InteractionMatrix

-- D --

defaultBuffer	Return default buffer If InteractionArray is supplied, it uses the dimensions of counts matrices to set the buffer dimensions.
dim-method	InteractionJaggedArray Class
dim-method	JaggedArray Class

-- E --

end1	Access each portion of a GInteractions-like object
end1-method	Access each portion of a GInteractions-like object
end2	Access each portion of a GInteractions-like object
end2-method	Access each portion of a GInteractions-like object

-- F --

findOverlaps	Overlap methods for InteractionJaggedArray
findOverlaps-method	Overlap methods for InteractionJaggedArray

-- H --

hdf5BlockApply	HDF5-backed blockApply
hdf5BlockApply-method	HDF5-backed blockApply

-- I --

InteractionArray	InteractionArray Class
InteractionArray-class	InteractionArray Class
InteractionArray-method	InteractionArray Class
InteractionJaggedArray	InteractionJaggedArray Class
InteractionJaggedArray-class	InteractionJaggedArray Class
InteractionMatrix	InteractionMatrix Class
InteractionMatrix-class	InteractionMatrix Class
InteractionMatrix-method	InteractionMatrix Class
interactions-method	InteractionJaggedArray Class

-- J --

JaggedArray	JaggedArray Class
JaggedArray-class	JaggedArray Class

-- L --

length-method

InteractionJaggedArray Class

-- M --

makeGInteractionsFromDataFrame	Convert DataFrames to GInteraction objects
makeGInteractionsFromDataFrame-method	Convert DataFrames to GInteraction objects
makeRandomGInteractions	Creating random GRanges & GInteractions
makeRandomGInteractions-method	Creating random GRanges & GInteractions
makeRandomGRanges	Creating random GRanges & GInteractions
makeRandomGRanges-method	Creating random GRanges & GInteractions
mariner	Mariner: Explore the Hi-Cs
MatrixSelection	MatrixSelection Class
MatrixSelection-class	MatrixSelection Class
MergedGInteractions	MergedGInteractions Class
MergedGInteractions-class	MergedGInteractions Class
mergePairs	Merge sets of paired interactions
mergePairs-method	Merge sets of paired interactions
metadata-method	InteractionJaggedArray Class

-- O --

overlapsAny	Overlap methods for InteractionJaggedArray
overlapsAny-method	Overlap methods for InteractionJaggedArray

-- P --

path-method	InteractionJaggedArray Class
path-method	JaggedArray Class
path-method	Accessor for h5File path from an InteractionMatrix
path<--method	Accessor for h5File path from an InteractionMatrix
pileupBoundaries	Pileup Hi-C contacts around boundary regions
pileupBoundaries-method	Pileup Hi-C contacts around boundary regions
pileupDomains	Pileup Hi-C domains
pileupDomains-method	Pileup Hi-C domains
pileupPixels	Pileup Hi-C pixels
pileupPixels-method	Pileup Hi-C pixels
pixelsToMatrices	Expand pixels to submatrices
pixelsToMatrices-method	Expand pixels to submatrices
plotEnrichment	Adjust loop enrichment to remove distance- dependent effect.
plotEnrichment-method	Adjust loop enrichment to remove distance- dependent effect.
plotMatrix	Plot matrix
plotMatrix-method	Plot matrix
pullHicMatrices	Pull submatrices from '.hic' files
pullHicMatrices-method	Pull submatrices from '.hic' files
pullHicPixels	Pull contact frequency from '.hic' files
pullHicPixels-method	Pull contact frequency from '.hic' files

-- R --

rbind-method	InteractionArray Class
rbind-method	InteractionMatrix Class
regularize	Regularize JaggedArray or InteractionJaggedArray objects
regularize-method	Regularize JaggedArray or InteractionJaggedArray objects
removeShortPairs	Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal.
removeShortPairs-method	Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal.

-- S --

selectBlock	Visualize selection for a MatrixSelection object
selectBlock-method	Visualize selection for a MatrixSelection object
selectBottomLeft	Visualize selection for a MatrixSelection object
selectBottomLeft-method	Visualize selection for a MatrixSelection object
selectBottomRight	Visualize selection for a MatrixSelection object
selectBottomRight-method	Visualize selection for a MatrixSelection object
selectCenterPixel	Visualize selection for a MatrixSelection object
selectCenterPixel-method	Visualize selection for a MatrixSelection object
selectCols	Visualize selection for a MatrixSelection object
selectCols-method	Visualize selection for a MatrixSelection object
selectCoordinates	Visualize selection for a MatrixSelection object
selectCoordinates-method	Visualize selection for a MatrixSelection object
selectCorners	Visualize selection for a MatrixSelection object
selectCorners-method	Visualize selection for a MatrixSelection object
selectInner	Visualize selection for a MatrixSelection object
selectInner-method	Visualize selection for a MatrixSelection object
selectionMethod	Get selectionMethod from MergedGInteractions object
selectionMethod-method	Get selectionMethod from MergedGInteractions object
selectOuter	Visualize selection for a MatrixSelection object
selectOuter-method	Visualize selection for a MatrixSelection object
selectPixel	Get the pixel representing the strongest or weakest interaction in an InteractionArray
selectPixel-method	Get the pixel representing the strongest or weakest interaction in an InteractionArray
selectRadius	Visualize selection for a MatrixSelection object
selectRadius-method	Visualize selection for a MatrixSelection object
selectRows	Visualize selection for a MatrixSelection object
selectRows-method	Visualize selection for a MatrixSelection object
selectSubmatrix	Visualize selection for a MatrixSelection object
selectSubmatrix-method	Visualize selection for a MatrixSelection object
selectTopLeft	Visualize selection for a MatrixSelection object
selectTopLeft-method	Visualize selection for a MatrixSelection object
selectTopRight	Visualize selection for a MatrixSelection object
selectTopRight-method	Visualize selection for a MatrixSelection object
seqnames1	Access each portion of a GInteractions-like object
seqnames1-method	Access each portion of a GInteractions-like object
seqnames2	Access each portion of a GInteractions-like object
seqnames2-method	Access each portion of a GInteractions-like object
sets	Get each set from a MergedGInteractions object
sets-method	Get each set from a MergedGInteractions object
shiftRanges	Flexibly shifting GRanges according to strand
shiftRanges-method	Flexibly shifting GRanges according to strand
show-method	InteractionArray Class
show-method	InteractionJaggedArray Class
show-method	InteractionMatrix Class
show-method	JaggedArray Class
show-method	Visualize selection for a MatrixSelection object
snapToBins	Snap GRanges or GInteractions to nearest bins
snapToBins-method	Snap GRanges or GInteractions to nearest bins
sources	Accessor for sources
sources-method	Accessor for sources
start1	Access each portion of a GInteractions-like object
start1-method	Access each portion of a GInteractions-like object
start2	Access each portion of a GInteractions-like object
start2-method	Access each portion of a GInteractions-like object
subsetByOverlaps	Overlap methods for InteractionJaggedArray
subsetByOverlaps-method	Overlap methods for InteractionJaggedArray

-- misc --

[-method	InteractionJaggedArray Class
[-method	JaggedArray Class