Package: methylumi 2.53.0
Sean Davis
methylumi: Handle Illumina methylation data
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Authors:
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methylumi.pdf |methylumi.html✨
methylumi/json (API)
| # Install 'methylumi' in R: |
| install.packages('methylumi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/seandavi/methylumi/issues
On BioConductor:methylumi-2.53.0(bioc 3.21)methylumi-2.52.0(bioc 3.20)
dnamethylationtwochannelpreprocessingqualitycontrolcpgisland
Last updated 2 months agofrom:491e60ef08. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:.mclapplybetasbetas<-combinecombine27k450kcontrolDatacontrolData<-controlTypescorplotcy3Cy3.NCy3<-cy5Cy5.NCy5<-dataTypedataType<-designIItoMandUdesignItoMandUdetectiondetection<-diagnosticsestimateMexprsexprs<-extractBarcodeAndPositionfeatureFiltergetAssayDataNameSubstitutionsgetBarcodesgetHistoryhistIDATsToMatricesIDATtoMatrixintensities.IBintensities.Mintensities.OOBintensities.OOB.allelicintensities.UintensitiesByChannellumiCSVlumIDATmergeProbeDesignsmethylatedmethylated.Nmethylated.N<-methylated<-methylumi.bgcorrmethylumi.diagnosticsmethylumiCSVmethylumIDATmethylumiRNChannelSetToMethyLumiSetnegctlsnegctls.stderrnegnormnormalizeMethyLumiSetnormctlspairsplotNAsplotNegOobplotSampleIntensitiesprobeNAspsummarypval.detectpval.detect<-pvalspvals<-qc.probe.plotQCdataQCdata<-qcplotsampleNAsshowstripBeadNsstripBeadSDsstripMethyLumiSetstripOOBsummarytcgaPipelinetotal.intensityunmethylatedunmethylated.Nunmethylated.N<-unmethylated<-varFilter
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrfansifarverfastmapFDb.InfiniumMethylation.hg19foreachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfimulttestmunsellnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Handle Illumina methylation data | methylumi-package methylumi |
| Data frame describing loci on the 27 and 450k arrays. | CpGs |
| Estimate methylation M-value matrix | estimateM |
| Extract the Barcode and Position Information from Sentrix ID | extractBarcodeAndPosition |
| Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object | featureFilter featureFilter,MethyLumiM-method featureFilter,MethyLumiSet-method |
| Return a data.frame of AssayData name substitutions. | getAssayDataNameSubstitutions |
| convert multiple idats to matrices | IDATsToMatrices |
| process a single IDAT (just the mean intensities) | IDATtoMatrix |
| Class '"methylData"', superclass for MethyLumiSet and MethyLumiM | diagnostics,methylData-method methylated.N,methylData-method methylated.N<-,methylData,matrix-method methylData-class plotNAs,methylData-method pval.detect,methylData-method pval.detect<-,methylData,numeric-method unmethylated.N,methylData-method unmethylated.N<-,methylData,matrix-method |
| methylumi accessors | betas betas<- corplot getHistory methylated methylated<- pvals pvals<- QCdata QCdata<- unmethylated unmethylated<- |
| The base class for storing Illumina Methylation data | methylated,MethyLumi-method methylated<-,MethyLumi,matrix-method MethyLumi-class pvals,MethyLumi-method pvals<-,MethyLumi,matrix-method qcplot,Methylumi-method summary,MethyLumi-method unmethylated,MethyLumi-method unmethylated<-,MethyLumi,matrix-method |
| Strip excessive probe-level data from MethyLumiSets | stripBeadNs stripBeadSDs stripMethyLumiSet stripOOB |
| methylumIDAT | methylumIDAT |
| Generics defined in methylumi | betas,GenomicMethylSet-method betas,MethylSet-method betas,RangedSummarizedExperiment-method combine27k450k controlData controlData<- cy3 Cy3.N Cy3<- cy5 Cy5.N Cy5<- dataType dataType<- designIItoMandU designItoMandU detection detection<- diagnostics getBarcodes getProtocolData IDATsToDFs IDATtoDF intensities.IB intensities.M intensities.OOB intensities.OOB.allelic intensities.U intensitiesByChannel lumiCSV lumIDAT mergeProbeDesigns methylated,MethylSet-method methylated.N methylated.N<- methylumi.bgcorr methylumi.diagnostics methylumiCSV NChannelSetToMethyLumiSet negctls negctls.stderr negnorm normctls plotNAs plotNegOob probeNAs psummary pval.detect pval.detect<- qc.probe.plot sampleNAs total.intensity unmethylated,MethylSet-method unmethylated.N unmethylated.N<- |
| Class "MethyLumiM": for Illumina Methylation microarray data using logRatios | betas,MethyLumiM-method combine,MethyLumiM,MethyLumiM-method controlData,MethyLumiM-method controlData<-,MethyLumiM,ANY-method controlTypes,MethyLumiM-method dataType,MethyLumiM-method dataType<-,MethyLumiM,ANY-method dataType<-,MethyLumiM-method detection,MethyLumiM-method detection<-,MethyLumiM-method getHistory,MethyLumiM-method intensitiesByChannel,MethyLumiM-method methylated,MethyLumiM-method methylated.N,MethyLumiM-method methylated.N<-,MethyLumiM,ANY-method methylated<-,MethyLumiM,ANY-method MethyLumiM MethyLumiM-class negctls,MethyLumiM,character-method negctls,MethyLumiM,missing-method negnorm,MethyLumiM,character-method negnorm,MethyLumiM,missing-method normctls,MethyLumiM-method probeNAs,MethyLumiM-method pvals,MethyLumiM-method QCdata,MethyLumiM-method sampleNAs,MethyLumiM-method total.intensity,MethyLumiM-method unmethylated,MethyLumiM-method unmethylated.N,MethyLumiM-method unmethylated.N<-,MethyLumiM,ANY-method unmethylated<-,MethyLumiM,ANY-method [,MethyLumiM,ANY,ANY,ANY-method [,MethyLumiM,ANY-method |
| Class '"MethyLumiQC"' for holding Illumina methylation QC data | combine,MethyLumiQC,MethyLumiQC-method controlData<-,MethyLumiSet,MethyLumiQC-method controlTypes,MethyLumiQC-method Cy3.N,MethyLumiQC-method Cy3<-,MethyLumiQC,matrix-method Cy5.N,MethyLumiQC-method Cy5<-,MethyLumiQC,matrix-method hist,MethyLumiQC-method intensitiesByChannel,MethyLumiQC-method methylated,MethyLumiQC-method MethyLumiQC-class negctls,MethyLumiQC,character-method negctls,MethyLumiQC,missing-method negctls.stderr,MethyLumiQC,character-method negctls.stderr,MethyLumiQC,missing-method negnorm,MethyLumiQC,character-method negnorm,MethyLumiQC,missing-method normctls,MethyLumiQC-method QCdata<-,MethyLumiSet,MethyLumiQC-method qcplot,MethyLumiQC-method unmethylated,MethyLumiQC-method |
| Load data from Illumina methylation platform | methylumiR |
| Class '"MethyLumiSet"' for containing Illumina methylation data | betas,MethyLumiSet-method betas<-,MethyLumiSet,matrix-method boxplot,MethyLumiSet-method combine,MethyLumiSet,MethyLumiSet-method combine27k450k,MethyLumiSet,MethyLumiSet-method controlData,MethyLumiSet-method controlData<-,MethyLumiSet controlTypes,MethyLumiSet-method corplot,MethyLumiSet-method Cy3.N,MethyLumiSet-method Cy5.N,MethyLumiSet-method exprs,MethyLumiSet-method getHistory,MethyLumiSet-method hist,MethyLumiSet-method intensities.IB,MethyLumiSet,character-method intensities.IB,MethyLumiSet,missing-method intensities.M,MethyLumiSet,character-method intensities.M,MethyLumiSet,missing-method intensities.OOB,MethyLumiSet,character-method intensities.OOB,MethyLumiSet,missing-method intensities.OOB.allelic,MethyLumiSet,character,character-method intensities.OOB.allelic,MethyLumiSet,missing,missing-method intensities.U,MethyLumiSet,character-method intensities.U,MethyLumiSet,missing-method intensitiesByChannel,MethyLumiSet-method methylated,MethyLumiSet-method methylated<-,MethyLumiSet,matrix-method MethyLumiSet-class negctls,MethyLumiSet,character-method negctls,MethyLumiSet,missing-method negctls.stderr,MethyLumiSet,character-method negctls.stderr,MethyLumiSet,missing-method negnorm,MethyLumiSet,character-method negnorm,MethyLumiSet,missing-method normctls,MethyLumiSet-method pairs,MethyLumiSet-method plotSampleIntensities,MethyLumiSet-method probeNAs,MethyLumiSet-method QCdata,MethyLumiSet-method QCdata<-,MethyLumiSet qcplot,MethyLumiSet-method sampleNAs,MethyLumiSet-method show,MethyLumiSet-method total.intensity,MethyLumiSet-method unmethylated,MethyLumiSet-method unmethylated<-,MethyLumiSet,matrix-method [,MethyLumiSet,ANY,ANY,ANY-method [,MethyLumiSet,ANY-method |
| Example SAM format Illumina methylation dataset | mldat |
| Normalize a MethyLumiSet, accounting for dye bias | normalizeMethyLumiSet |
| Plot the sample intensities. | plotSampleIntensities |
| Methods for dealing with control data for Illumina methylation data. | controlTypes qcplot |
| Total convenience function for processing IDATs like tcga | tcgaPipeline |
| Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object | varFilter varFilter,MethyLumiM-method varFilter,MethyLumiSet-method |
