Package: minfi 1.59.1
Kasper Daniel Hansen
minfi: Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
Authors:
minfi_1.59.1.tar.gz
minfi_1.59.1.zip(r-4.7)minfi_1.59.1.zip(r-4.6)minfi_1.59.1.zip(r-4.5)
minfi_1.59.1.tgz(r-4.6-any)minfi_1.59.1.tgz(r-4.5-any)
minfi_1.59.1.tar.gz(r-4.7-any)minfi_1.59.1.tar.gz(r-4.6-any)
minfi_1.59.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
minfi/json (API)
NEWS
| # Install 'minfi' in R: |
| install.packages('minfi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hansenlab/minfi/issues
On BioConductor:minfi-1.59.0(bioc 3.24)minfi-1.58.0(bioc 3.23)
immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol
Last updated from:fa38de7846. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 615 | ||
| linux-devel-x86_64 | NOTE | 971 | ||
| source / vignettes | OK | 759 | ||
| linux-release-x86_64 | NOTE | 952 | ||
| macos-release-arm64 | NOTE | 666 | ||
| macos-oldrel-arm64 | NOTE | 428 | ||
| windows-devel | NOTE | 801 | ||
| windows-release | NOTE | 948 | ||
| windows-oldrel | NOTE | 731 | ||
| wasm-release | OK | 557 |
Exports:addQCaddSexaddSnpInfoannotationannotation<-bgcorrect.illuminablockFinderbumphuntercoercecombinecombineArrayscompartmentscontrolStripPlotconvertArraycpgCollapsecreateCorMatrixdensityBeanPlotdensityPlotdetectionPdmpFinderdropLociWithSnpsdropMethylationLociestimateCellCountsextractABfeatureNamesfeatureNames<-fixMethOutliersgaphunterGenomicMethylSetGenomicRatioSetgetAnnotationgetAnnotationObjectgetBetagetCNgetControlAddressgetGenomicRatioSetFromGEOgetGreengetIslandStatusgetLocationsgetMgetManifestgetManifestInfogetMethgetMethSignalgetNBeadsgetOOBgetProbeInfogetProbeTypegetQCgetRedgetSexgetSnpBetagetSnpInfogetUnmethIlluminaMethylationAnnotationIlluminaMethylationManifestilogit2initializelogit2makeGenomicRatioSetFromMatrixmapToGenomemdsPlotMethylSetminfiQCnormalize.illumina.controlpDatapData<-plotBetasByTypeplotCpgplotQCplotSexpreprocessFunnormpreprocessIlluminapreprocessMethodpreprocessNoobpreprocessQuantilepreprocessRawpreprocessSWANqcReportratioConvertRatioSetread.450kread.450k.expread.450k.sheetread.metharrayread.metharray.expread.metharray.sheetreadGEORawFilereadTCGARGChannelSetRGChannelSetExtendedsampleNamessampleNames<-showsubsetByLoci
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimemulttestnlmenor1mixopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analyze Illumina's methylation arrays | minfi-package minfi |
| Finds blocks of methylation differences for Illumina methylation arrays | blockFinder |
| Methods for function 'bumphunter' in Package 'minfi' | bumphunter,GenomicRatioSet-method |
| A method for combining different types of methylation arrays into a virtual array. | combineArrays combineArrays,GenomicMethylSet,GenomicMethylSet-method combineArrays,GenomicRatioSet,GenomicRatioSet-method combineArrays,MethylSet,MethylSet-method combineArrays,RatioSet,RatioSet-method combineArrays,RGChannelSet,RGChannelSet-method |
| Estimates A/B compartments from Illumina methylation arrays | compartments createCorMatrix extractAB |
| Plot control probe signals. | controlStripPlot |
| A method for converting a type of methylation arrays into a virtual array of another type. | convertArray convertArray,GenomicMethylSet-method convertArray,GenomicRatioSet-method convertArray,MethylSet-method convertArray,RatioSet-method convertArray,RGChannelSet-method |
| Collapse methylation values of adjacent CpGs into a summary value. | cpgCollapse |
| Density bean plots of methylation Beta values. | densityBeanPlot |
| Density plots of methylation Beta values. | densityPlot |
| Detection p-values for all probed genomic positions. | detectionP |
| Find differentially methylated positions | dmpFinder |
| Cell Proportion Estimation | estimateCellCounts |
| Fix methylation outliers | fixMethOutliers |
| Find gap signals in 450k data | gaphunter |
| GenomicMethylSet instances | annotation,GenomicMethylSet-method annotation<-,GenomicMethylSet,ANY-method combine,GenomicMethylSet,GenomicMethylSet-method featureNames,GenomicMethylSet-method featureNames<-,GenomicMethylSet-method GenomicMethylSet GenomicMethylSet-class getBeta,GenomicMethylSet-method getCN,GenomicMethylSet-method getM,GenomicMethylSet-method getMeth,GenomicMethylSet-method getUnmeth,GenomicMethylSet-method mapToGenome,GenomicMethylSet-method pData,GenomicMethylSet-method pData<-,GenomicMethylSet,DataFrame-method preprocessMethod,GenomicMethylSet-method sampleNames,GenomicMethylSet-method sampleNames<-,GenomicMethylSet,ANY-method show,GenomicMethylSet-method |
| GenomicRatioSet instances | annotation,GenomicRatioSet-method annotation<-,GenomicRatioSet,ANY-method combine,GenomicRatioSet,GenomicRatioSet-method featureNames,GenomicRatioSet-method featureNames<-,GenomicRatioSet-method GenomicRatioSet GenomicRatioSet-class getBeta,GenomicRatioSet-method getCN getCN,GenomicRatioSet-method getM,GenomicRatioSet-method mapToGenome,GenomicRatioSet-method pData,GenomicRatioSet-method pData<-,GenomicRatioSet,DataFrame-method preprocessMethod,GenomicRatioSet-method sampleNames,GenomicRatioSet-method sampleNames<-,GenomicRatioSet,ANY-method show,GenomicRatioSet-method |
| Accessing annotation for Illumina methylation objects | addSnpInfo dropLociWithSnps getAnnotation getAnnotationObject getIslandStatus getLocations getProbeType getSnpInfo |
| Reading Illumina methylation array data from GEO. | getGenomicRatioSetFromGEO |
| Various utilities | getMethSignal |
| Estimate sample-specific quality control (QC) for methylation data | addQC getQC plotQC |
| Estimating sample sex based on methylation data | addSex getSex plotSex |
| Class 'IlluminaMethylationAnnotation' | getManifest,IlluminaMethylationAnnotation-method IlluminaMethylationAnnotation IlluminaMethylationAnnotation-class show,IlluminaMethylationAnnotation-method |
| Class '"IlluminaMethylationManifest"' | getControlAddress getManifest getManifest,character-method getManifest,IlluminaMethylationManifest-method getManifestInfo getProbeInfo IlluminaMethylationManifest IlluminaMethylationManifest-class show,IlluminaMethylationManifest-method |
| logit in base 2. | ilogit2 logit2 |
| Make a GenomicRatioSet from a matrix | makeGenomicRatioSetFromMatrix |
| Mapping methylation data to the genome | mapToGenome mapToGenome,MethylSet-method mapToGenome,RatioSet-method mapToGenome,RGChannelSet-method mapToGenome-methods |
| Multi-dimensional scaling plots giving an overview of similarities and differences between samples. | mdsPlot |
| MethylSet instances | annotation,MethylSet-method annotation<-,MethylSet,ANY-method combine,MethylSet,MethylSet-method dropMethylationLoci featureNames,MethylSet-method featureNames<-,MethylSet-method getBeta getBeta,MethylSet-method getCN,MethylSet-method getM getM,MethylSet-method getManifest,MethylSet-method getMeth getMeth,MethylSet-method getUnmeth getUnmeth,MethylSet-method MethylSet MethylSet-class pData,MethylSet-method pData<-,MethylSet,DataFrame-method preprocessMethod preprocessMethod,MethylSet-method sampleNames,MethylSet-method sampleNames<-,MethylSet,ANY-method show,MethylSet-method |
| Defunct functions in package 'minfi' | minfi-defunct read.450k read.450k.exp read.450k.sheet |
| Deprecated functions in package 'minfi' | minfi-deprecated |
| easy one-step QC of methylation object | minfiQC |
| Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types. | plotBetasByType |
| Plot methylation values at an single genomic position | plotCpg |
| Functional normalization for Illumina 450k arrays | preprocessFunnorm |
| Perform preprocessing as Genome Studio. | bgcorrect.illumina normalize.illumina.control preprocessIllumina |
| The Noob/ssNoob preprocessing method for Infinium methylation microarrays. | preprocessNoob |
| Stratified quantile normalization for an Illumina methylation array. | preprocessQuantile |
| Creation of a MethylSet without normalization | preprocessRaw |
| Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips | preprocessSWAN |
| QC report for Illumina Infinium Human Methylation 450k arrays | qcReport |
| Converting methylation signals to ratios (Beta or M-values) | ratioConvert ratioConvert,GenomicMethylSet-method ratioConvert,MethylSet-method ratioConvert-methods |
| RatioSet instances | annotation,RatioSet-method annotation<-,RatioSet,ANY-method combine,RatioSet,RatioSet-method featureNames,RatioSet-method featureNames<-,RatioSet-method getBeta,RatioSet-method getCN,RatioSet-method getM,RatioSet-method pData,RatioSet-method pData<-,RatioSet,DataFrame-method preprocessMethod,RatioSet-method RatioSet RatioSet-class sampleNames,RatioSet-method sampleNames<-,RatioSet,ANY-method show,RatioSet-method |
| Parsing IDAT files from Illumina methylation arrays. | read.metharray |
| Reads an entire metharray experiment using a sample sheet | read.metharray.exp |
| Reading an Illumina methylation sample sheet | read.metharray.sheet |
| Read in Unmethylated and Methylated signals from a GEO raw file. | readGEORawFile |
| Read in tab deliminited file in the TCGA format | readTCGA |
| Class '"RGChannelSet"' | annotation,RGChannelSet-method annotation<-,RGChannelSet,ANY-method coerce,RGChannelSetExtended,RGChannelSet-method combine,RGChannelSet,RGChannelSet-method featureNames,RGChannelSet-method featureNames<-,RGChannelSet-method getBeta,RGChannelSet-method getGreen getManifest,RGChannelSet-method getNBeads getOOB getRed getSnpBeta pData,RGChannelSet-method pData<-,RGChannelSet,DataFrame-method RGChannelSet RGChannelSet-class RGChannelSetExtended RGChannelSetExtended-class sampleNames,RGChannelSet-method sampleNames<-,RGChannelSet,ANY-method show,RGChannelSet-method |
| Subset an RGChannelset by CpG loci. | subsetByLoci |
