Function reference • mariner

About mariner

mariner mariner-package: Mariner: Explore the Hi-Cs

Manipulating Paired Ranges

Convert, bin, and shift paired genomic ranges

as_ginteractions() makeGInteractionsFromDataFrame(): Convert DataFrames to GInteraction objects

shiftRanges(): Flexibly shifting GRanges according to strand

binRanges(): Flexibly bin ranges

assignToBins(): Flexibly bin paired ranges

snapToBins(): Snap GRanges or GInteractions to nearest bins

seqnames1() seqnames2() start1() end1() start2() end2(): Access each portion of a GInteractions-like object

makeRandomGRanges() makeRandomGInteractions(): Creating random GRanges & GInteractions

Clustering & Merging Interactions

Group nearby interactions and select one as representative

mergePairs(): Merge sets of paired interactions

MergedGInteractions-class MergedGInteractions: MergedGInteractions Class

aggMetadata(): Aggregate the metadata columns of merged pairs

clusters(): Get clustered pairs from MergedGInteractions object

sources(): Accessor for sources

sets(): Get each set from a MergedGInteractions object

Extracting & Aggregating Interactions

Pull Hi-C pixels or matrices, then aggregate by files or interactions

pullHicPixels(): Pull contact frequency from `.hic` files

InteractionMatrix() show(<InteractionMatrix>) rbind(<InteractionMatrix>) cbind(<InteractionMatrix>): InteractionMatrix Class

pixelsToMatrices(): Expand pixels to submatrices

removeShortPairs(): Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal.

pullHicMatrices(): Pull submatrices from `.hic` files

InteractionArray() show(<InteractionArray>) rbind(<InteractionArray>) cbind(<InteractionArray>): InteractionArray Class

counts(<InteractionArray>) counts(<InteractionMatrix>) `counts<-`(<InteractionMatrix>): Access count matrices from InteractionArray or InteractionMatrix

path(<InteractionMatrix>) `path<-`(<InteractionMatrix>): Accessor for h5File path from an InteractionMatrix

show(<InteractionJaggedArray>) dim(<InteractionJaggedArray>) interactions(<InteractionJaggedArray>) metadata(<InteractionJaggedArray>) colData(<InteractionJaggedArray>) counts(<InteractionJaggedArray>) path(<InteractionJaggedArray>) length(<InteractionJaggedArray>) `[`(<InteractionJaggedArray>,<ANY>,<ANY>,<ANY>): InteractionJaggedArray Class

show(<JaggedArray>) `[`(<JaggedArray>,<ANY>,<ANY>,<ANY>) as.list(<JaggedArray>) path(<JaggedArray>) dim(<JaggedArray>): JaggedArray Class

findOverlaps(<InteractionJaggedArray>,<InteractionJaggedArray>) findOverlaps(<InteractionJaggedArray>,<Vector>) findOverlaps(<InteractionJaggedArray>,<missing>) countOverlaps(<InteractionJaggedArray>,<InteractionJaggedArray>) countOverlaps(<InteractionJaggedArray>,<Vector>) countOverlaps(<InteractionJaggedArray>,<missing>) overlapsAny(<InteractionJaggedArray>,<InteractionJaggedArray>) overlapsAny(<InteractionJaggedArray>,<Vector>) overlapsAny(<InteractionJaggedArray>,<missing>) subsetByOverlaps(<InteractionJaggedArray>,<InteractionJaggedArray>) subsetByOverlaps(<InteractionJaggedArray>,<Vector>) subsetByOverlaps(<InteractionJaggedArray>,<missing>): Overlap methods for InteractionJaggedArray

regularize(): Regularize JaggedArray or InteractionJaggedArray objects

aggHicMatrices(): Aggregate count matrices from InteractionArray objects

hdf5BlockApply(): HDF5-backed blockApply

plotMatrix(): Plot matrix

Pileup analysis

Wraps several mariner functions to facilitate pileup analysis of Hi-C pixels, domains or boundaries.

pileupPixels(): Pileup Hi-C pixels

pileupDomains(): Pileup Hi-C domains

pileupBoundaries(): Pileup Hi-C contacts around boundary regions

Calculating Loop Enrichment

Determine loop enrichment to local background with selection functions to flexibility select foreground and background.

calcLoopEnrichment(): Calculate loop enrichment over background.

plotEnrichment() adjustEnrichment(): Adjust loop enrichment to remove distance- dependent effect.

Selection functions

MatrixSelection-class MatrixSelection: MatrixSelection Class

selectRadius() selectCenterPixel() selectSubmatrix() selectCoordinates() selectBlock() selectTopLeft() selectTopRight() selectBottomRight() selectBottomLeft() selectCorners() selectRows() selectCols() selectInner() selectOuter() show(<MatrixSelection>): Visualize selection for a MatrixSelection object

selectionMethod(): Get selectionMethod from MergedGInteractions object

defaultBuffer(): Return default buffer If InteractionArray is supplied, it uses the dimensions of counts matrices to set the buffer dimensions.

Miscellaneous

changePixelRes(): Change pixels from one resolution to another selecting the new pixel using Hi-C data.

selectPixel(): Get the pixel representing the strongest or weakest interaction in an InteractionArray