NEWS.md

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mesa 0.5.1

This is the first released version on github, following a lengthy period of internal development. Many things have changed in a major overhaul of the package.

BUG FIXES

• summariseDMRsByGene now correctly summarises genes when they have different positions or lengths in different windows.
• plotCorrelationMatrix no longer crashes when no annotation is being used.

mesa 0.5.0

ADDED

• Examples added for some functions, and documentation for some related functions merged.
• Added more tests following inspection of covr coverage.
• getPCA() and getUMAP() now return an object of class mesaDimRed, which wraps the previous list based output. This object now contains a copy of the sampleTable, which may be edited using mutate and left_join.
• A new example qseaSet for a small portion of the mouse genome.
• Added the ability to specifying a biomaRt object directly on a qseaSet for used for finding gene annotation in plotGeneHeatmap.

CHANGES

• plotPCA() and plotUMAP() no longer require passing the qseaSet, as the sampleTable is stored in the object.
• Added functions setMesaGenome, setMesaTxDb and setMesaAnnoDb to set global defaults for the annotation packages required by annotateWindows. This has the effect that annotateWindows will no longer assume hg38 by default with no arguments.
• summariseDMRsByGene function now requires annotateWindows to have already been called on the DMRs (previously it called this internally if necessary).
• Reduced the number of messages produced when generating tables of data.

BUG FIXES

• poolSamples now returns data frames instead of matrices in the libraries slot.
• select now works when dropping a column.
• PCA/UMAP functions now give a more informative error if there are insufficient regions or samples.
• downSample now works correctly again following changes to how table and enframe interact.
• calculateDMRs now correctly returns an empty data frame if no DMRs are found.

mesa 0.4.1

BUG FIXES

• plotPCA now works when colouring by a factor variable
• mutate now cannot be used to change the sample_name in the sample table of a qseaSet which breaks the object. renameQsetNames or renameSamples must be used for this.

CHANGES

• HMMCopy related functions now take explicit input of the GC and mappability tracks, rather than having hardcoded internal hg38 objects, allowing for different genomes.
• Removed the data objects gc_hg38_10kb and map_hg38_10kb (GC and mappability tracks for hg38 at 10kb resolution) for package size reasons.

mesa 0.4.0

BUG FIXES

• Fixed how the relative enrichment (relH/GoGe) calculation is performed (addMedipsEnrichmentFactors) when using the qsea default method for reads (#1).

• Filtering a qseaSet now works correctly when a qseaSet has no cnv data.

• Fixed pull to work directly on a qseaSet to return a column of the sampleTable.

CHANGES

• Removed mutateQset, filterQset, arrangeQset, sortQset, pullQset, leftJoinQset as these just work on the dplyr verbs directly.

• Combined getBetaMeans and getNormalisedReadSum into new function called summariseAcrossWindows. This allows an arbitrary function to be (e.g. mean or sd) to be applied over all the windows in each sample, and returns a data frame with one result per sample.

• Added a new function addSummaryAcrossWindows that performs summariseAcrossWindows but returns the qseaSet with the results added to the sampleTable.

• Added a function asValidGranges that checks if an object can be coerced to a GRanges object and does so if possible.

• Added setMesaGenome function to globally set which genome to be used for plotting functions.

• Standardised on using "Windows" instead of "Regions". For instance, filterRegions is now filterWindows, and plotGRangesHeatmap is now plotRegionsHeatmap. Added a function getWindows to mimic getRegions from qsea.

• Complete overhaul of the PCA functionality.

  • This is now split into two functions, getPCA and plotPCA, and the getPCAwithBatch function has been removed.

• UMAP functionality added, using the same framework as PCAs, with getUMAP and getPCA. This is still experimental.

• Changed pivotDMRsLonger to return columns "group1" and "group2" instead of "sample1" and "sample2".

• In DMR results, moved the betaDelta columns to be after the equivalent adjPval columns instead of all being at the end.

• Renamed the contrastsToDo argument of makeDMRs to just contrasts.

• mixSamples (formerly mixQsetSamples) no longer sets type and tumour in the sampleTable of the returned qseaSet.

• Changes to heatmap plotting functions (plotRegionsHeatmap and plotGeneHeatmap, plotCNVHeatmap):

  • plotGRangesHeatmap is now renamed as plotRegionsHeatmap

  • Both support a useGroups argument, to determine whether to average over the "group" column of the sampleTable or not.

  • Argument signatureGR of plotRegionsHeatmap changed to regionsToOverlap.

  • Changed from pheatmap package to ComplexHeatmap package for the plotting.

  • The method of adding sample annotations has been overhauled. This is now specified using sampleAnnotation (instead of annotationCol), and does not support the use of the getAnnotationDataFrame function. These options now directly take the name of the features to be plotted, supporting unquoted tidy evaluation, i.e. all of these work:

    • sampleAnnotation = group

    • sampleAnnotation = c(group, type)

    • sampleAnnotation = c("group","type")

  • Heatmaps can now have windows annotated with the use of windowAnnotation. This supports unquoted tidy evaluation as well, and can use anything on the qseaSet regions slot or on the regionsToOverlap argument.

  • The getAnnotationDataFrame and getAnnotationDataFrameIndividual functions have been removed.

  • The colours for the annotations have been overhauled. These now try to choose appropriate colour scales for continuous data based on whether they are strictly positive or not. For discrete annotations, the colours are set globally for the entire annotation set, to try and prevent the occurrance of different annotations using very similar colours.

• getDataTable function can now keep the suffix (e.g. _nrpm or _beta) if required.

• removeWindowsOverCutoff and keepWindowsOverCutoff have been replaced by a more general function called subsetWindowsBySignal. This allows for a general function to be specified (for instance mean or max) as well as a threshold, enabling for the filtering of windows based on that function.

• Parallelisation of functions is now controlled explicitly by the setMesaParallel function. This must be used to enable multicore evaluation.

• When calculating DMRs, by default the qseaSet will now be filtered to only include samples which are present in the contrasts for the calculating of the dispersion estimates in the generalised linear model. This can be controlled by the calcDispersionAll option. The pre-filtering of windows based on expression is unchanged - this only uses samples included in the contrasts.

• The difference in mean beta values in the DMR output has been renamed from betaDelta to deltaBeta to reflect the mathematical usage \tex{\Delta \beta}.

• Updated documentation in many functions.

• Authors updated to include Paddy Harker, Kevin Brennan and Katarzyna Kamieniecka.

• Removed exporting of internal functions: dropAvgFragDetails, getBamCoveragePairedAndUnpairedR1, mixThreeQsetSamples, getCGPositions, fitQseaGLM, getDMRsData, subsetWindowsOverBackground

• Renamed many functions throughout the package:

  Previous Function Name	New Function Name
  addQseaNormalisationSteps	addNormalisation
  annotateData	annotateWindows
  calculateArrayBetas	convertToArrayBetaTable
  calculateCpGEnrichment	calculateCGEnrichment
  calculateCpGEnrichmentGRanges	calculateCGEnrichmentGRanges
  countWindowsOverCutoff	countWindowsAboveCutoff
  downsampleQsea	downSample
  filterRegions	filterWindows
  liftOverhg19	liftOverHg19
  mixQsetSamples	mixSamples
  plotDMRUpSet	plotDMRUpset
  qseaWriteDMRsBeds	writeDMRsToBed
  qseaWriteDMRsExcel	writeDMRsToExcel
  relabelQset	renameSamples
  summariseByGene	summariseDMRsByGene

• Six functions have been replaced by different functions (detailed above)

  +---------------------------+--------------------------+ | Previous Function | Replacement Function(s) | +===========================+==========================+ | getQseaPCA | getPCA/plotPCA | | | | | getPCAwithBatch | | +---------------------------+--------------------------+ | getBetaMeans | summariseAcrossWindows | | | | | getNormalisedReadSum | | +---------------------------+--------------------------+ | removeWindowsOverCutoff | subsetWindowsBySignal | | | | | keepWindowsOverCutoff | | +---------------------------+--------------------------+

• Renamed data objects:

  Previous data name	New data name
  encodeBlacklist	ENCODEbadRegions
  examplePairedTumourQset	exampleTumourNormal

mesa 0.2.3

CHANGES

• plotGeneHeatmap now uses bioMaRt to find the gene details, based on the genome or mart supplied.

• filterByOverlaps now works when the `qseaSet` regions contains "chr" but the regions to filter by do not or vice versa.

• Removed all references to PooledControl sample (previously suggested for normalisation).

• Various R CMD check warning issues fixed.

• filterByOverlaps no longer allows the option to take a list of window ID numbers.

• Fixed addMedipsEnrichmentFactors function inside makeQset when using the "qseaPaired" coverageMethod.

• Fixed tests for addMedipsEnrichmentFactors

mesa 0.2.2

BUG FIXES

• Update mixQsetSamples to match the mixArrayWithQset code (and now runs with latest version of R).
• Less stringent checking on the p values being zero bug in qsea, to minimise false positives.

KNOWN ISSUES

* pull is not working directly, pullQset must be used.

mesa 0.2.1

Version set for initial release in v2.0.1 of the internal CBC Nextflow pipeline.