Package: mesa 0.99.5

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_0.99.5.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

Datasets:

On CRAN:

Conda:

sequencingdnamethylationcpgislandpreprocessingnormalizationqualitycontrolvisualizationcopynumbervariationdifferentialmethylationcoveragechipseqchiponchip

3.24 score 86 exports 189 dependencies

Last updated from:61c890a583. Checks:8 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING569
linux-devel-x86_64WARNING857
source / vignettesERROR809
linux-release-x86_64WARNING834
macos-release-arm64WARNING537
macos-oldrel-arm64WARNING677
windows-devel-x86_64WARNING671
windows-release-x86_64WARNING659
windows-oldrel-x86_64WARNING780
wasm-releaseOK509

Exports:%>%addBamCoveragePairedAndUnpairedaddHMMcopyCNVaddHyperStableFractionaddLibraryInformationaddMedipsEnrichmentFactorsaddNormalisationaddSummaryAcrossWindowsannotateWindowsasValidGrangescalculateCGEnrichmentcalculateCGEnrichmentGRangescalculateDMRscalculateFractionReadsInGRangescalculateGenomicCGDistributioncolnamescombineQsetscombineQsetsListconvertToArrayBetaTablecountWindowsAboveCutoffdownSamplefilterByNonOverlapsfilterByOverlapsfilterWindowsfitQseaGLMgetBetaTablegetCountTablegetDataTablegetDimRedgetDMRsDatagetGenomicFeatureDistributiongetMartgetMesaAnnoDbgetMesaGenomegetMesaParallelgetMesaTxDbgetNRPMTablegetPatterngetPCAgetSampleQCSummarygetUMAPgetWindowNamesgetWindowsis.qseaSetliftOverHg19makeAllContrastsmakeQsetmakeTransposedTablemesaDimRedmesaPCAmesaUMAPmixSamplespivotDMRsLongerplotCNVheatmapplotCorrelationMatrixplotDimRedplotDMRUpsetplotGeneHeatmapplotGenomicFeatureDistributionplotPCA.mesaDimRedplotRegionsHeatmapplotUMAPpoolSamplesqseaTableToChrGRangesremoveCNVremoveLibraryFactorsremoveNormMethodSuffixrenameQsetNamesrenameSamplesrunHMMCopyselectQsetsetMartsetMesaAnnoDbsetMesaGenomesetMesaParallelsetMesaTxDbsliceDMRssubsetQsetsubsetWindowsBySignalsubsetWindowsOverBackgroundsummariseAcrossWindowssummariseDMRsByContrastsummariseDMRsByGenewriteBigWigswriteDMRsToBedwriteDMRsToExcel

Dependencies:abindAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootBSgenomebslibcachemcaToolsChIPseekercigarillocirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdoParallelDOSEdplyrenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgridGraphicsgsongtablegtoolshighrHMMcopyhmshtmltoolshtmlwidgetshttrhttr2huesigraphIRangesisobanditeratorsjanitorjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpatchworkpheatmappillarpkgconfigplotrixplyrplyrangespngpolyclipprettyunitsprogresspurrrqseaR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfoshapesnakecasesnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstibbletidydrtidyrtidyselecttidytreetimechangetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlyulab.utilszoo

Readme and manuals

Help Manual

Help pageTopics
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) from MEDIPSgetCGPositions
Get counts per windowgetCountTable
Extract per-window data (counts / NRPM / beta)getDataTable
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
Get window names from a qseaSet or ranges/tablegetWindowNames
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