Package: mesa 0.99.8

Steven Hill

mesa: Methylation Enrichment Sequencing Analysis

A package for the analysis of methylation enrichment sequencing data (e.g. MBD-seq or MEDIP-seq). This allows for the window-based evaluation of methylation levels (using the 'qsea' package), including functions for determining differentially methylated regions. Many functions are provided for tidyverse style modification of the qseaSet objects originally defined in 'qsea'.

Authors:Simon Pearce [aut], Steven Hill [aut, cre], Paddy Harker [ctb], Kevin Brennan [ctb], Katarzyna Kamieniecka [ctb], Felipe Perez Martinez [ctb], Cancer Research UK National Biomarker Centre [cph, fnd]

mesa_0.99.8.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mesa/json (API)

# Install 'mesa' in R:
install.packages('mesa', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cruk-mi/mesa/issues

Pkgdown/docs site:https://cruk-mi.github.io

Datasets:

On CRAN:

Conda:

sequencingdnamethylationcpgislandpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationdifferentialmethylationcoveragechipseqchiponchip

5.44 score 17 scripts 92 exports 183 dependencies

Last updated from:dc949639e7. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE496
linux-develOK896
source / vignettesOK713
linux-releaseOK880
macos-releaseOK805
macos-oldrelOK954
windows-develOK882
windows-releaseOK742
windows-oldrelOK528
wasm-releaseOK348

Exports:%>%addBamCoveragePairedAndUnpairedaddHMMcopyCNVaddHyperStableFractionaddLibraryInformationaddMedipsEnrichmentFactorsaddNormalisationaddSummaryAcrossWindowsannotateWindowsas.data.frameasValidGrangescalculateCGEnrichmentcalculateCGEnrichmentGRangescalculateDMRscalculateFractionReadsInGRangescalculateGenomicCGDistributioncolnamescombineQsetscombineQsetsListconvertToArrayBetaTablecountWindowsAboveCutoffdownSamplefilterByNonOverlapsfilterByOverlapsfilterWindowsfitQseaGLMgetBetaTablegetCoordinatesgetCountTablegetDataTablegetDimRedgetDMRsDatagetGenomicFeatureDistributiongetMartgetMesaAnnoDbgetMesaGenomegetMesaParallelgetMesaTxDbgetNRPMTablegetParametersgetPatterngetPCAgetPrcompgetResultsgetSampleQCSummarygetSampleTablegetUMAPgetWindowNamesgetWindowsis.qseaSetliftOverHg19makeAllContrastsmakeQsetmakeTransposedTablemesaDimRedmesaPCAmesaUMAPmixSamplespivotDMRsLongerplotCNVheatmapplotCorrelationMatrixplotDimRedplotDMRUpsetplotGeneHeatmapplotGenomicFeatureDistributionplotPCA.mesaDimRedplotRegionsHeatmapplotUMAPpoolSamplesqseaTableToChrGRangesremoveCNVremoveLibraryFactorsremoveNormMethodSuffixrenameQsetNamesrenameSamplesrunHMMCopyselectQsetsetMartsetMesaAnnoDbsetMesaGenomesetMesaParallelsetMesaTxDbsliceDMRssubsetQsetsubsetWindowsBySignalsubsetWindowsOverBackgroundsummariseAcrossWindowssummariseDMRsByContrastsummariseDMRsByGenewriteBigWigswriteDMRsToBedwriteDMRsToExcel

Dependencies:AnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootBSgenomebslibcachemcaToolsChIPseekercigarillocirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrdigestdoParallelDOSEdplyrenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgridGraphicsgsongtablegtoolshighrHMMcopyhmshtmltoolshtmlwidgetshttrhttr2huesigraphIRangesisobanditeratorsjanitorjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalubridatemagrittrMASSMatrixmatrixStatsmemoisemimenlmeopensslpatchworkpheatmappillarpkgconfigplotrixplyrplyrangespngpolyclipprettyunitsprogresspurrrqseaR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4VectorsS7sassscalesscatterpieSeqinfoshapesnakecasesnowstatmodstringistringrsyssystemfontstibbletidydrtidyrtidyselecttidytreetimechangetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlyulab.utilszoo

Dimensionality Reduction - PCAs and UMAPs
PCA functions | Basic use | Editing the sampleTable | plotPCA() function arguments | Annotating samples by colour and/or shape | Colour and shape palettes | NA values | Components | Point size | Text annotations | Output of getPCA() | getPCA() function arguments | Setting number of top variable windows to use | Samples used to calculate variability | Inputting a pre-calculated dataTable | Normalisation Method | Filtering regions | UMAPs | Session info
Rendered frompca.Rmdusingknitr::rmarkdown

Last update: 2026-10-15
Started: 2026-03-20

Data Tables and Quality Control
Generating tables of values from a qseaSet | Quality Control | Relative Enrichment | Fragments without pattern | Hyper-stably methylated regions | Summary | Session info
Rendered fromdata-and-qc.Rmdusingknitr::rmarkdown

Last update: 2026-10-13
Started: 2026-03-20

Differentially Methylated Regions and Annotation
Differentially Methylated Regions | Introduction | Output | Covariates | Additional Options | Annotation | Other Genomes | Analysing DMRs | Summarising by Gene | Plotting Windows | Session info
Rendered fromdifferentially-methylated-regions.Rmdusingknitr::rmarkdown

Last update: 2026-10-08
Started: 2026-03-20

Generating qseaSets
Introduction | Sample Metadata | Making a qseaSet | Selecting the windows | Coverage-related options | Note on Proper Pairs | Copy Number Variation | Calculating CpG Density | Offset Reads | Beta Calculation Fitting | Note on TMM Normalisation | Session info
Rendered fromgeneration.Rmdusingknitr::rmarkdown

Last update: 2026-10-08
Started: 2026-03-20

Introduction to Mesa
Introduction | Example Dataset | Parts of a qseaSet | Sample Table | Counts Matrix | Windows | Library Information | Copy Number Variation | Parameters, Enrichment, Zygosity | Parallelisation | Session info
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2026-10-08
Started: 2026-03-20

Readme and manuals

Help Manual

Help pageTopics
mesa: Methylation Enrichment Sequencing Analysismesa-package mesa
Add coverage to a qseaSet using proper pairs and/or high-quality R1 readsaddBamCoveragePairedAndUnpaired
Add per-sample CNV calls to a qseaSet using HMMcopyaddHMMcopyCNV
Summarise the fraction of hyper-stable methylated regions (GRCh38 only)addHyperStableFraction
Add library metrics to the qseaSet sample tableaddLibraryInformation
Add MEDIPS-style enrichment metrics to a qseaSet sample tableaddMedipsEnrichmentFactors
Add qsea normalisation steps with defaultsaddNormalisation
Append window summaries to the sample tableaddSummaryAcrossWindows
Annotate genomic windows using ChIPseeker (with optional CpG/FANTOM context)annotateWindows
Arrange (reorder) samples in a qseaSet via dplyr syntaxarrange.qseaSet
Coerce common tabular inputs to GRangesasValidGranges
Pre-calculated CpG distribution values for BSgenomesBSgenome.Hsapiens.NCBI.GRCh38.CpG.distribution BSgenome.Hsapiens.UCSC.hg19.CpG.distribution BSgenome.Mmusculus.UCSC.mm10.CpG.distribution
CpG enrichment from a BAM file (MEDIPS-style)calculateCGEnrichment
CpG enrichment from GRanges of reads (MEDIPS-style)calculateCGEnrichmentGRanges
Fit GLM and return DMR data in one stepcalculateDMRs
Fraction of thresholded windows overlapping a set of regionscalculateFractionReadsInGRanges
Genome-wide CpG statistics (relH and GoGe)calculateGenomicCGDistribution
Column names of a qseaSet sample tablecolnames,qseaSet-method
Combine two qseaSetscombineQsets
Combine multiple qseaSetscombineQsetsList
Convert qsea beta values to array-like probe matrixconvertToArrayBetaTable
Count windows above a cutoffcountWindowsAboveCutoff
Downsample reads in a qseaSetdownSample
2019 ENCODE list of poorly mapped regions in hg38ENCODEbadRegions
A small example qseaSet with 5 paired tumour/normal samples.exampleMouse
A small example qseaSet with 5 paired tumour/normal samples.exampleTumourNormal
FANTOM5 regions for GRCh38FantomRegions
Filter samples in a qseaSetfilter.qseaSet
Subset a qseaSet by overlaps / non-overlaps with genomic regionsfilterByNonOverlaps filterByOverlaps
Filter regions (windows) inside a qseaSetfilterWindows
Fit a generalized linear model (GLM) to a qseaSetfitQseaGLM
GC content across the human genome (hg38/GRCh38)gc_hg38_1000kb gc_hg38_500kb gc_hg38_50kb
Get beta per windowgetBetaTable
Genomic positions of a motif (CG)getCGPositions
Get counts per windowgetCountTable
Extract per-window data (counts / NRPM / beta)getDataTable getDataTable,ANY-method getDataTable,mesaDimRed-method
Extract DMR-level results from a fitted GLMgetDMRsData
Summarise signal by genomic contextgetGenomicFeatureDistribution
Get annotation DB for current or specified genomegetMesaAnnoDb
Get current mesa genome settinggetMesaGenome
Get TxDb for current or specified genomegetMesaTxDb
Get NRPM per windowgetNRPMTable
Infer pattern names from region density columnsgetPattern
Generate a PCA from a qseaSetgetDimRed getPCA getUMAP
Summarise key QC fields per samplegetSampleQCSummary
Accessors for dimensionality reduction resultsas.data.frame,mesaDimRed-method dimRedAccessors getCoordinates getCoordinates,mesaDimRed-method getCoordinates,mesaPCA-method getCoordinates,mesaUMAP-method getParameters,mesaDimRed-method getPrcomp getPrcomp,mesaDimRed-method getPrcomp,mesaPCA-method getResults getResults,mesaDimRed-method getSampleNames,mesaDimRed-method getSampleNames,mesaPCA-method getSampleNames,mesaUMAP-method getSampleTable,mesaDimRed-method
Get window names from a qseaSet, ranges/table or dimensionality reduction objectgetWindowNames getWindowNames,ANY-method getWindowNames,mesaDimRed-method getWindowNames,mesaPCA-method getWindowNames,mesaUMAP-method
Extract the regions (windows) used in a qseaSetgetWindows
hg19tohg38 liftover chainhg19ToHg38.over.chain
Infinium 450k probe locations for hg38.hg38_450kArrayGR
CpG islands for hg38.hg38CpGIslands
Ultra-stable methylated regions (GRCh38)hg38UltraStableProbes
Check whether an object is a qseaSetis.qseaSet
Left-join onto the sample table of a mesaDimRedleft_join.mesaDimRed
Left join data onto a qseaSet sample tableleft_join.qseaSet
Lift over genomic ranges from hg19 to hg38liftOverHg19
Generate all possible pairwise contrastsmakeAllContrasts
Construct an initial qseaSet from BAMs and metadatamakeQset
Make a wide sample-by-window tablemakeTransposedTable
Mappability across the human genome (hg38/GRCh38)map_hg38_1000kb map_hg38_500kb map_hg38_50kb
Dimensionality reduction results containermesaDimRed mesaDimRed-class show,mesaDimRed-method
PCA results containermesaPCA mesaPCA-class show,mesaPCA-method
UMAP results containermesaUMAP mesaUMAP-class show,mesaUMAP-method
Mix two samples to generate a synthetic qseaSet samplemixSamples
Mutate the sample table of a mesaDimRedmutate.mesaDimRed
Mutate columns in a qseaSet sample tablemutate.qseaSet
Transform DMR results to long formatpivotDMRsLonger
CNV heatmap across samplesplotCNVheatmap
Sample correlation heatmapplotCorrelationMatrix
Plot dimensionality reduction resultsplotDimRed
UpSet plot of DMR overlapsplotDMRUpset
Plot sample signal over windows spanning a gene (± flanks) as a heatmap using *ComplexHeatmap*. The gene can be given as a HGNC symbol or Ensembl ID.plotGeneHeatmap
Distribution of windows across genomic featuresplotGenomicFeatureDistribution
Plot principal component analysis (PCA) resultsplotPCA.mesaDimRed
Heatmap of signal across selected genomic regionsplotRegionsHeatmap
Plot UMAP resultsplotUMAP
Pool (merge) samples that share a common name prefixpoolSamples
Pull a column from a qseaSet sample tablepull.qseaSet
Convert a makeTable-like data frame to GRanges (UCSC style)qseaTableToChrGRanges
Remove (zero out) CNV data from a qseaSetremoveCNV
Set library factors to 1removeLibraryFactors
Remove normalisation suffix from column namesremoveNormMethodSuffix
Rename samples in a qseaSet by regexrenameQsetNames
Rename samples using a column from the sample tablerenameSamples
Run HMMcopy on per-window reads for a single samplerunHMMCopy
Select or rename columns in a qseaSet sample tableselect.qseaSet
Select or rename columns of a qseaSet sample tableselectQset
Set or get an Ensembl/BioMart handle on a qseaSetgetMart getMart,qseaSet-method setMart setMart,qseaSet-method
Set default OrgDb (annoDb) for downstream annotation helperssetMesaAnnoDb
Set default genome for downstream annotation helperssetMesaGenome
Manage mesa parallelisation (set & query)getMesaParallel setMesaParallel
Set default TxDb for downstream annotation helperssetMesaTxDb
Take the top most DMRs per contrast, based on those with the largest value of the selected metricsliceDMRs
Sort samples in a qseaSetsort.qseaSet
Subset a qseaSet by samplessubsetQset
Subset windows in a qseaSet by signal across samplessubsetWindowsBySignal
Subset windows above Poisson backgroundsubsetWindowsOverBackground
Summarise across windows per samplesummariseAcrossWindows
Summarise DMRs by contrastsummariseDMRsByContrast
Summarise DMRs by genesummariseDMRsByGene
Write bigWig tracks per sample or groupwriteBigWigs
Write DMR results to BED fileswriteDMRsToBed
Write DMR results to an Excel workbookwriteDMRsToExcel