Package index • mesa

All functions
`BSgenome.Hsapiens.UCSC.hg19.CpG.distribution` `BSgenome.Hsapiens.NCBI.GRCh38.CpG.distribution` `BSgenome.Mmusculus.UCSC.mm10.CpG.distribution`	Pre-calculated CpG distribution values for BSgenomes
`ENCODEbadRegions`	2019 ENCODE list of poorly mapped regions in hg38
`FantomRegions`	FANTOM5 regions for GRCh38
`addBamCoveragePairedAndUnpaired()`	Add coverage to a qseaSet using proper pairs and/or high-quality R1 reads
`addHMMcopyCNV()`	Add per-sample CNV calls to a qseaSet using HMMcopy
`addHyperStableFraction()`	Summarise the fraction of hyper-stable methylated regions (GRCh38 only)
`addLibraryInformation()`	Add library metrics to the qseaSet sample table
`addMedipsEnrichmentFactors()`	Add MEDIPS-style enrichment metrics to a qseaSet sample table
`addNormalisation()`	Add qsea normalisation steps with defaults
`addSummaryAcrossWindows()`	Append window summaries to the sample table
`filterByOverlaps()` `filterByNonOverlaps()`	Subset a qseaSet by overlaps / non-overlaps with genomic regions
`annotateWindows()`	Annotate genomic windows using ChIPseeker (with optional CpG/FANTOM context)
`arrange(<qseaSet>)`	Arrange (reorder) samples in a qseaSet via dplyr syntax
`asValidGranges()`	Coerce common tabular inputs to GRanges
`calculateCGEnrichment()`	CpG enrichment from a BAM file (MEDIPS-style)
`calculateCGEnrichmentGRanges()`	CpG enrichment from GRanges of reads (MEDIPS-style)
`calculateDMRs()`	Fit GLM and return DMR data in one step
`calculateFractionReadsInGRanges()`	Fraction of thresholded windows overlapping a set of regions
`calculateGenomicCGDistribution()`	Genome-wide CpG statistics (relH and GoGe)
`colnames(<qseaSet>)`	Column names of a qseaSet sample table
`combineQsets()`	Combine two qseaSets
`combineQsetsList()`	Combine multiple qseaSets
`convertToArrayBetaTable()`	Convert qsea beta values to array-like probe matrix
`countWindowsAboveCutoff()`	Count windows above a cutoff
`getSampleTable(<mesaDimRed>)` `getSampleNames(<mesaDimRed>)` `getResults()` `getParameters(<mesaDimRed>)` `getCoordinates()` `getSampleNames(<mesaPCA>)` `getSampleNames(<mesaUMAP>)` `getPrcomp()` `as.data.frame(<mesaDimRed>)`	Accessors for dimensionality reduction results
`downSample()`	Downsample reads in a qseaSet
`exampleMouse`	A small example qseaSet with 5 paired tumour/normal samples.
`exampleTumourNormal`	A small example qseaSet with 5 paired tumour/normal samples.
`filter(<qseaSet>)`	Filter samples in a qseaSet
`filterWindows()`	Filter regions (windows) inside a qseaSet
`fitQseaGLM()`	Fit a generalized linear model (GLM) to a qseaSet
`gc_hg38_1000kb` `gc_hg38_500kb` `gc_hg38_50kb`	GC content across the human genome (hg38/GRCh38)
`getBetaTable()`	Get beta per window
`getCGPositions()`	Genomic positions of a motif (CG)
`getCountTable()`	Get counts per window
`getDMRsData()`	Extract DMR-level results from a fitted GLM
`getDataTable()`	Extract per-window data (counts / NRPM / beta)
`getPCA()` `getUMAP()` `getDimRed()`	Generate a PCA from a qseaSet
`getGenomicFeatureDistribution()`	Summarise signal by genomic context
`getMesaAnnoDb()`	Get annotation DB for current or specified genome
`getMesaGenome()`	Get current mesa genome setting
`getMesaTxDb()`	Get TxDb for current or specified genome
`getNRPMTable()`	Get NRPM per window
`getPattern()`	Infer pattern names from region density columns
`getSampleQCSummary()`	Summarise key QC fields per sample
`getWindowNames()`	Get window names from a qseaSet, ranges/table or dimensionality reduction object
`getWindows()`	Extract the regions (windows) used in a qseaSet
`hg19ToHg38.over.chain`	hg19tohg38 liftover chain
`hg38CpGIslands`	CpG islands for hg38.
`hg38UltraStableProbes`	Ultra-stable methylated regions (GRCh38)
`hg38_450kArrayGR`	Infinium 450k probe locations for hg38.
`is.qseaSet()`	Check whether an object is a qseaSet
`left_join(<mesaDimRed>)`	Left-join onto the sample table of a mesaDimRed
`left_join(<qseaSet>)`	Left join data onto a qseaSet sample table
`liftOverHg19()`	Lift over genomic ranges from hg19 to hg38
`makeAllContrasts()`	Generate all possible pairwise contrasts
`makeQset()`	Construct an initial qseaSet from BAMs and metadata
`makeTransposedTable()`	Make a wide sample-by-window table
`map_hg38_1000kb` `map_hg38_500kb` `map_hg38_50kb`	Mappability across the human genome (hg38/GRCh38)
`mesa` `mesa-package`	mesa: Methylation Enrichment Sequencing Analysis
`mesaDimRed()` `show(<mesaDimRed>)`	Dimensionality reduction results container
`mesaPCA()` `show(<mesaPCA>)`	PCA results container
`mesaUMAP()` `show(<mesaUMAP>)`	UMAP results container
`mixSamples()`	Mix two samples to generate a synthetic qseaSet sample
`mutate(<mesaDimRed>)`	Mutate the sample table of a mesaDimRed
`mutate(<qseaSet>)`	Mutate columns in a qseaSet sample table
`pivotDMRsLonger()`	Transform DMR results to long format
`plotCNVheatmap()`	CNV heatmap across samples
`plotCorrelationMatrix()`	Sample correlation heatmap
`plotDMRUpset()`	UpSet plot of DMR overlaps
`plotDimRed()`	Plot dimensionality reduction results
`plotGeneHeatmap()`	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.
`plotGenomicFeatureDistribution()`	Distribution of windows across genomic features
`plotPCA.mesaDimRed()`	Plot principal component analysis (PCA) results
`plotRegionsHeatmap()`	Heatmap of signal across selected genomic regions
`plotUMAP()`	Plot UMAP results
`poolSamples()`	Pool (merge) samples that share a common name prefix
`pull(<qseaSet>)`	Pull a column from a qseaSet sample table
`qseaTableToChrGRanges()`	Convert a makeTable-like data frame to GRanges (UCSC style)
`removeCNV()`	Remove (zero out) CNV data from a qseaSet
`removeLibraryFactors()`	Set library factors to 1
`removeNormMethodSuffix()`	Remove normalisation suffix from column names
`renameQsetNames()`	Rename samples in a qseaSet by regex
`renameSamples()`	Rename samples using a column from the sample table
`runHMMCopy()`	Run HMMcopy on per-window reads for a single sample
`select(<qseaSet>)`	Select or rename columns in a qseaSet sample table
`selectQset()`	Select or rename columns of a qseaSet sample table
`setMart()` `getMart()`	Set or get an Ensembl/BioMart handle on a qseaSet
`setMesaAnnoDb()`	Set default OrgDb (annoDb) for downstream annotation helpers
`setMesaGenome()`	Set default genome for downstream annotation helpers
`setMesaParallel()` `getMesaParallel()`	Manage mesa parallelisation (set & query)
`setMesaTxDb()`	Set default TxDb for downstream annotation helpers
`sliceDMRs()`	Take the top most DMRs per contrast, based on those with the largest value of the selected metric
`sort(<qseaSet>)`	Sort samples in a qseaSet
`subsetQset()`	Subset a qseaSet by samples
`subsetWindowsBySignal()`	Subset windows in a qseaSet by signal across samples
`subsetWindowsOverBackground()`	Subset windows above Poisson background
`summariseAcrossWindows()`	Summarise across windows per sample
`summariseDMRsByContrast()`	Summarise DMRs by contrast
`summariseDMRsByGene()`	Summarise DMRs by gene
`writeBigWigs()`	Write bigWig tracks per sample or group
`writeDMRsToBed()`	Write DMR results to BED files
`writeDMRsToExcel()`	Write DMR results to an Excel workbook

Reference

All functions