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.
plotMatrix() to accept na.colorBug 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:
selectCenterPixelselectRadiusselectSubmatrixselectCoordinatesselectBlockselectTopLeftselectTopRightselectBottomRightselectBottomLeftselectCornersselectRowsselectColsselectInnerselectOutercalcLoopEnrichment 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.
Methods for pulling Hi-C pixels and matrices from .hic files and storing them on-disk with HDF5Array and DelayedArray.
New or updated functions:
snapToBins()
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).
counts() accessor for matrix.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.
counts() accessor for submatrices.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().
First pre-release of mariner functionality focused on manipulating, clustering, and merging paired interactions.
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
getPairClusters
selectionMethod
sources
subsetBySource