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Changelog

Source: NEWS.md

footprintR 0.3.8

  • Add Signal to Noise Ratio read-level statistics and filtering options to calcReadStats, filterReads and filterReadsBam
  • Add Signal to Noise Ratio window aggregate statistics for quantifying footprint coherence with estimateSNRwindows

footprintR 0.3.7

  • Add argument orderReverse to allow reversing the order in which reads are displayed in read-level plots
  • Add argument randomSubset to subsetReads to allow random selection of a given number or fraction of reads

footprintR 0.3.6

  • Filter out reads without modified-base calls if maxFracLowConf or maxEntropy filters are set in filterReads or filterReadsBam

footprintR 0.3.5

  • Add argument orderRegion and orderReads = "region" to read-level plotting functions to sort reads by average modification probabilities in a specified window
  • Add argument minCoveredFraction to filterReads() and plotRegion()
  • Add argument fillColors to read-level plotting functions to control colors of modification probabilities
  • Add arguments clustDist and windowWidth to read-level plotting functions for more fine-grained control of clustering

footprintR 0.3.4

footprintR 0.3.3

  • Add argument arglistFootprints replacing and extending footprintColors in plotRegion()
  • Various smaller improvements and bug fixes

footprintR 0.3.2

  • Add removeAllNApos argument to filterReads and subsetReads
  • Add BigWig plot panel
  • Add regroupReads function to regroup reads by an annotation
  • Rewrite and expand genome scanning framework

footprintR 0.3.1

  • Explicitly ignore supplementary and secondary alignments in all reading modes in readModBam()
  • Various smaller improvements and bug fixes

footprintR 0.3.0

  • Enable use of more flexible region specification in readModBam()
  • Add additional supported statistics in flattenReadLevelAssay() (Sum and Mean)
  • Various smaller improvements and bug fixes

footprintR 0.2.5

  • Expand readModBam() to allow direct extraction of summary values (Nmod, Nvalid), and to use the pileup approach for quick extraction of read-level values
  • Add filterReadsBam() to filter-out reads from input bam files and write reads that pass all filters to output bam files
  • Add functions to statistically identify differentially modified regions (scanForHighScoringRegions() and helpers)

footprintR 0.2.4

  • Speed up plotRegion() for data sets with many reads by replacing do.call() with a faster alternative
  • Add option to adjust facet heights to the number of reads in the facet
  • Add option to squish the reads (put more than one read in a row, if possible)
  • Change the orderReads argument for read-level plots from a logical to a character indicating the type of ordering

footprintR 0.2.3

  • Add addFootprints() and helper functions calcFootprintScores() and segmentFootprintScores()
  • Add sampleAnnot argument to reading functions to enable inclusion of additional sample annotations
  • Add trim argument to readModBam, to restrict the returned object to the specified regions
  • Enable plotting of read-specific (footprint) regions

footprintR 0.2.2

  • Rename the facetBySample argument to the read-level plots to facetBy, allowing facetting by an arbitrary sample column
  • Add groupBy and colorBy argument to the summary plots, for specification of arbitrary sample columns to group and color values by
  • Open up for using other smoothing methods, specified via the smoothMethod argument to the summary plots. Add ‘rollingMean’ as a first alternative to the smoothing splines
  • Add progress bars and expand messages to track progress when reading modbam files

footprintR 0.2.1

  • Refactor calcReadStats() (non-user facing changes)
  • Add genomic region track type to plotRegion() and expose more arguments for the individual track types
  • Export helper functions to create individual plotRegion() tracks
  • Modify plotRegion() to display exactly the provided input region (with minimal padding, and not restricting to the subregion with observed data)
  • Add support for relative coordinate system in plotRegion()
  • Use 0.5 instead of 1.0 as the label distance between non-overlapping reads
  • Modify getAnchorRegions() to return a RangedSummarizedExperiment object, allow the user to set the anchor name

footprintR 0.2.0

  • Harmonize function and argument names (using camelCase)
  • Use BiocParallel::BPPARAM in functions that support parallel execution
  • Rename addReadsSummary() to flattenReadLevelAssay()

footprintR 0.1.4

  • Refactor plotRegion() to use a single tracks argument instead of tracks.summary and tracks.reads.
  • Allow filterReads() to return the filter statistics table without subsetting the SummarizedExperiment object.
  • Add readModBam(..., variantPositions) argument that adds labels to reads, enabling allele specific analyses.

footprintR 0.1.3

  • Add option to decompress bam records in readModBam() in parallel on multiple threads.

footprintR 0.1.2

  • Add a NEWS.md file to track changes to the package.
  • Use SparseArray::NaArray assays to represent read-level modification probabilities.