# Mariner: Explore the Hi-Cs

## Documentation for package ‘mariner’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F H I J L M O P R S misc

mariner-package | 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