Changes in version 0.99.0                        

Bug fixes and improvements:

  - Improve dispatch speed of mergePairs() by removing S4 method
    dispatch on all arguments to just x and radius.

  - Fix bug in mergePairs() where all pairs are altered during mean of
    mode transformation. Now original pairs are preserved when accessed
    with getPairClusters().

  - Set replace method for counts<- accessor for InteractionMatrix
    objects. Helpful for converting DelayedMatrix to matrix.

  - Update pixelsToMatrix to preserve metadata columns and include some
    additional tests.

  - Add plotMatrix() function for plotting matrix data as a heatmap.
    Useful for visualizing DelayedMatrices from pullHicMatrices() and
    aggHicMatrices(). Compatible with plotgardener package.
    
      - Allow plotMatrix() to accept na.color

  - Bug fix in mergePairs() that allows columns named "radius" and/or
    "method".

  - Swap "binSize" and "files" argument order in pullHicPixels and
    pullHicMatrices

  - Allow pullHicPixels to overwrite existing HDF5 files.

  - Validity checks and functions to access/update the HDF5 paths for
    InteractionMatrix objects, even when those paths have been broken.

  - Add temporary plotBullseye function.

  - Selection functions for selecting indices of a matrix:
    
      - selectCenterPixel
      - selectRadius
      - selectSubmatrix
      - selectCoordinates
      - selectBlock
      - selectTopLeft
      - selectTopRight
      - selectBottomRight
      - selectBottomLeft
      - selectCorners
      - selectRows
      - selectCols
      - selectInner
      - selectOuter

  - calcLoopEnrichment function for flexibly calculating enrichment of
    interactions compared to their local background.

  - adjustEnrichment and plotEnrichment for adjusting the loop
    enrichment to remove the effect of loop size on enrichment and
    visualize this correction across chosen parameters.

                        Changes in version 0.2.0                        

Methods for pulling Hi-C pixels and matrices from .hic files and storing
them on-disk with HDF5Array and DelayedArray.

Overview of functionality

New or updated functions:

  - snapToBins()
    
      - "snaps" ranges in GInteractions objects to their nearest bin
        boundary. Allows spanning of multiple bins.

  - pullHicPixels() extracts contact frequency from .hic files and
    returns an InteractionMatrix object containing a matrix of Hi-C
    interactions (rows) and samples (columns).
    
      - Includes counts() accessor for matrix.
      - Custom show() method.
      - rbind() and cbind() methods.

  - pullHicMatrices() extracts submatrices of contact frequency from
    .hic files and returns an InteractionArray object containing a
    4-dimensional array of Hi-C submatrices, rownames, and colnames.
    
      - Includes counts() accessor for submatrices.
      - Custom show() method.
      - rbind() and cbind() methods.

  - pixelsToMatrices() takes GInteractions containing single pixels
    (i.e., each range represents one binSize) and expands ranges such
    that there is a buffer of pixels around each range.

  - changePixelRes() takes a GInteractions object containing pixels of
    interest and is resized to the from resolution/binSize (if its not
    already). Then count matrices are extracted for each interaction and
    .hic file using the new to resolution. Count matrices are aggregated
    by interactions with the supplied aggFUN and a new pixel is selected
    with the supplied selectFUN. Allows block processing for large
    datasets. The object returned is a GInteractions object with the
    updated pixel ranges along with a column containing the aggregated
    min/max value for that pixel.

  - calcLoopEnrichment() pulls Hi-C pixels and calculates the enrichment
    over background returning a DelayedMatrix of enrichment scores where
    rows are interactions and columns are Hi-C files.

  - Accessors for GInteractions objects such as seqnames1(), start1(),
    end1(), seqnames2(), start2(), end2().

                        Changes in version 0.1.0                        

First pre-release of mariner functionality focused on manipulating,
clustering, and merging paired interactions.

Overview of functionality

  - Conversion of paired-range data to GInteractions with
    as_ginteractions/makeGInteractionsFromDataFrame

  - Functions for manipulating GInteractions and GRanges objects with
    binPairs, binRanges, shiftRanges.

  - Functions for clustering and merging lists of GInteractions objects
    with mergePairs.

  - Extensions to GInteractions class with MergedGInteractions, and
    DelegatingGInteractions.

  - Accessor functions for MergedGInteractions:
    
      - aggPairMcols
          - Aggregate metadata columns of clustered interactions.
      - getPairClusters
          - Return interactions for each cluster of interactions.
      - selectionMethod
          - Method used to select pairs from each cluster of
            interactions.
      - sources
          - List of names (or indices) used as input for clustering and
            merging.
      - subsetBySource
          - Return interactions unique to each source or combination of
            sources.