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
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
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