rankedMatrix: New utility function for quickly performing ranked matrix calculations. Particularly useful for differential expression comparison across studies using log2 fold change or Wald test statistic.
aggregateCellsToSamples: Improved internal code for SummarizedExperiment metadata handling. Applies primarily to colData and rowData juggling for these methods.
interestingGroups: Reworked to define method against
SummarizedExperimentinherits from this class, supporting
mapCellsToSamples: Tightened up match assert checks.
mcolnamesnow uses S4 methods, primarily against
organism: Reworked S4 methods. Added support for
DataTableclasses from S4Vectors.
detectLanes: Renamed primary argument from
patternformal to evaluate
sampleData: Improved error message when
sampleNamefactor column is missing.
meltCounts: Switched from using
nonzeroGenesformal approach to
minCountsMethod, which is more flexible.
theme_paperwhiteare deprecated but exported with support, by suggesting acidplots package.
matchEnsemblReleaseToURL: Takes an Ensembl release version (e.g.
96) as input and returns the corresponding archive URL.
matchHumanOrthologs: Convenience function that wraps biomaRt package to map model system gene identifiers to HGNC IDs and symbols. This is particularly useful for running orthologus GSEA with our pfgsea package.
SummarizedExperimentnow includes all matrices defined in
assaysslot. Also improved support for
colDatahandling on subsets where
NAvalues have been removed.
theme_paperwhitedefunct, in favor if variants in new acidplots package.
combinemethod on SummarizedExperiment. Needed to ensure row names are assigned on rowData to provide backward compatibility for Bioc 3.7.
mapGenesToRownames: Improved matching for
SummarizedExperimentobjects that don’t contain gene-to-symbol mappings defined in
meltCounts: Improved factor handling. Also added
matrixmethod support. Added advanced option to disable
minCountsfiltering, by setting as