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Changelog

Source: NEWS.md

mariner 1.2.1

New features:

Added pileupBoundaries() for visualizing pileup Hi-C contacts in regions around genomic loci/boundary elements.

mariner 1.2.0

Breaking changes:

mariner 1.1.3

New features:

Wrapper functions for performing pileup analysis on pixels or domains.

  • pileupPixels() for extracting and aggregating Hi-C counts in square regions around pixels of interest (aggregate peak analysis).

  • pileupDomains() for extracting, resizing, and aggregating Hi-C counts in domain regions of interest (aggregate domain analysis).

Changes:

  • Improve documentation for removeShortPairs() to make it more clear that it should be run after any function that resizes interactions.

  • Add verbose option to regularize() to update users on regularization of jagged arrays.

mariner 1.1.2

Bug fixes:

  • Fix id mapping in aggPairMcols()

mariner 1.1.1

Bug fixes:

  • Fix in pullHic functions: After running .prepareInputs() which involves snapping ranges to bins, the adjusted ranges were not being used to calculate the expected matrix dimensions. This can sometimes cause a missmatch between the data used for enumerating bins, and the data that is extracted from the Hi-C file. Fixed by using the adjusted interactions to set the matrix dimensions.

mariner 1.1.0

New features:

  • JaggedArray and InteractionJaggedArray classes for irregular matrices.

  • Functions for generating random GRanges and GInteractions objects.

  • regularize method for converting irregular (i.e. jagged) to regular arrays.

  • New calcLoopEnrichment method for InteractionArray objects.

  • defaultBuffer() function for setting the buffer argument from an InteractionArray.

Bug Fixes:

  • Fix bug in removeShortPairs where padding wasn’t working as intended.

  • FUN argument of calcLoopEnrichment now accepts environmental variables and uses flexible argument names for fg and bg.

mariner 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 clusters().

  • 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.

  • 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.

mariner 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).

  • 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.

  • 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().

mariner 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.