Introduction | DNA methylation | High-throughput bisulfite sequencing | Basics | Reading the methylation call files | Reading the methylation call files and store them as flat file database | Reading the methylation calls from sorted Bismark alignments | Descriptive statistics on samples | Filtering samples based on read coverage | Comparative analysis | Merging samples | Sample Correlation | Clustering samples | Batch effects | Tiling windows analysis | Finding differentially methylated bases or regions | Correcting for overdispersion | Accounting for covariates | Finding differentially methylated bases using multiple-cores | Annotating differentially methylated bases or regions | Regional analysis | Convenience functions for annotation objects | methylKit convenience functions | Coercing methylKit objects to GRanges | Converting methylKit objects to methylDB objects and vice versa | Loading methylDB objects from tabix files | Selection: subsetting methylKit Objects | selectByOverlap | reorganize(): reorganizing samples and treatment vector within methylKit objects | percMethylation(): Getting percent methylation matrix from methylBase objects | methSeg(): segmentation of methylation or differential methylation profiles | Frequently Asked Questions | How can I select certain regions/bases from methylRaw or methylBase objects ? | How can I find if my regions of interest overlap with | How can I find the nearest TSS associated with my CpGs ? | How do you define promoters and CpG island shores ? | What does Bismark SAM output look like, where can I get more info ? | How can I reorder or remove samples at/from methylRawList or methylBase | Should I normalize my data ? | How can I force methylKit to use Fisher's exact test ? | Can use data from other aligners than Bismark in methylKit ? | Can I transform an methylKit object into an methylDB object ? | How could I share methylKit objects ? | Where do I find the flatfile database underlying a methylDB? | Why does my methylBaseDB flatfile database has a different name now ? | How can I make a bigwig file from methylKit result? | My data comes from MIRA-seq, can I use methylKit to perform the differential | My data comes from Methylation arrays, can I use methylKit to analyse my data ? | How can I analyze data generated from a local alignment ? | How can I analyze data generated from a spliced alignment ? | Why does the regionCount function not keep the input region order? | How can I merge muliple separate methylRaw objects into a methylRawList? | Acknowledgements | Full list of contributors | R session info | References
Package: methylKit 1.39.0
Altuna Akalin
methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
Authors:
methylKit_1.39.0.tar.gz
methylKit_1.39.0.zip(r-4.7)methylKit_1.39.0.zip(r-4.6)methylKit_1.39.0.zip(r-4.5)
methylKit_1.39.0.tgz(r-4.6-x86_64)methylKit_1.39.0.tgz(r-4.6-arm64)methylKit_1.39.0.tgz(r-4.5-x86_64)methylKit_1.39.0.tgz(r-4.5-arm64)
methylKit_1.39.0.tar.gz(r-4.7-arm64)methylKit_1.39.0.tar.gz(r-4.7-x86_64)methylKit_1.39.0.tar.gz(r-4.6-arm64)methylKit_1.39.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylKit/json (API)
| # Install 'methylKit' in R: |
| install.packages('methylKit', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/al2na/methylkit/issues
Uses libs:
Datasets:
- methylBase.obj - Example methylBase object.
- methylDiff.obj - Example methylKit objects.
- methylRawList.obj - Example methylRawList object.
On BioConductor:methylKit-1.39.0(bioc 3.24)methylKit-1.38.0(bioc 3.23)
dnamethylationsequencingmethylseqgenome-biologymethylationstatistical-analysisvisualizationcurlbzip2xz-utilszlibcpp
Last updated from:ac7f68d4b4. Checks:1 ERROR, 11 NOTE, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 292 | ||
| linux-devel-arm64 | NOTE | 409 | ||
| linux-devel-x86_64 | NOTE | 536 | ||
| source / vignettes | OK | 398 | ||
| linux-release-arm64 | NOTE | 433 | ||
| linux-release-x86_64 | NOTE | 545 | ||
| macos-release-arm64 | NOTE | 360 | ||
| macos-release-x86_64 | NOTE | 564 | ||
| macos-oldrel-arm64 | NOTE | 322 | ||
| macos-oldrel-x86_64 | NOTE | 700 | ||
| windows-devel | NOTE | 515 | ||
| windows-release | NOTE | 444 | ||
| windows-oldrel | NOTE | 490 | ||
| wasm-release | FAIL | 474 |
Exports:adjust.methylCadjustMethylCannotate.WithFeatureannotate.WithFeature.Flankannotate.WithGenicPartsassocCompbedgraphcalculateDiffMethcalculateDiffMethDSSclusterSamplesdataSimdiffMethPerChrfilterByCoverageget.methylDiffgetAssemblygetContextgetCorrelationgetCoverageStatsgetDatagetDBPathgetFeatsWithTargetsStatsgetFlanksgetMembersgetMethylationStatsgetMethylDiffgetSampleIDgetSampleID<-getTargetAnnotationStatsgetTreatmentgetTreatment<-joinSegmentNeighboursmakeMethylDBmethReadmethSegmethSeg2bedmethylRawListmethylRawListDBnormalizeCoveragePCASamplespercMethylationplotTargetAnnotationpoolprocessBismarkAlnreadread.bedread.bismarkread.feature.flankread.transcript.featuresreadMethylDBreconstructregionCountsremoveCompreorganizeselectselectByOverlaptileMethylCountsunite
Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodacodetoolscpp11crayoncurldata.tableDelayedArrayemdbookfarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemvtnormnlmenumDerivopensslplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adjust measured 5mC levels using 5hmC levels | adjustMethylC adjustMethylC,methylRaw,methylRaw-method adjustMethylC,methylRawDB,methylRawDB-method adjustMethylC,methylRawList,methylRawList-method adjustMethylC,methylRawListDB,methylRawListDB-method |
| Associate principal components with sample annotations | assocComp |
| Get bedgraph from methylRaw, methylRawList and methylDiff objects | bedgraph bedgraph,methylDiff-method bedgraph,methylDiffDB-method bedgraph,methylRaw-method bedgraph,methylRawDB-method bedgraph,methylRawList-method bedgraph,methylRawListDB-method |
| Calculate differential methylation statistics | calculateDiffMeth calculateDiffMeth,methylBase-method calculateDiffMeth,methylBaseDB-method |
| calculate Differential Methylation with DSS | calculateDiffMethDSS calculateDiffMethDSS,methylBase-method |
| Hierarchical Clustering using methylation data The function clusters samples using 'hclust' function and various distance metrics derived from percent methylation per base or per region for each sample. | clusterSamples clusterSamples,methylBase-method clusterSamples,methylBaseDB-method |
| Simulate DNA methylation data | dataSim |
| Get and plot the number of hyper/hypo methylated regions/bases per chromosome | diffMethPerChr diffMethPerChr,methylDiff-method diffMethPerChr,methylDiffDB-method |
| extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data | extract extract,methylBase,ANY-method extract,methylBaseDB,ANY-method extract,methylDiff,ANY-method extract,methylDiffDB,ANY-method extract,methylRaw,ANY-method extract,methylRawDB,ANY-method [,methylBase,ANY,ANY,ANY-method [,methylBaseDB,ANY,ANY,ANY-method [,methylDiff,ANY,ANY,ANY-method [,methylDiffDB,ANY,ANY,ANY-method [,methylRaw,ANY,ANY,ANY-method [,methylRawDB,ANY,ANY,ANY-method |
| Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage | filterByCoverage filterByCoverage,methylRaw-method filterByCoverage,methylRawDB-method filterByCoverage,methylRawList-method filterByCoverage,methylRawListDB-method |
| get assembly of the genome | getAssembly getAssembly,methylBase-method getAssembly,methylBaseDB-method getAssembly,methylDiff-method getAssembly,methylDiffDB-method getAssembly,methylRaw-method getAssembly,methylRawDB-method |
| get the context of methylation | getContext getContext,methylBase-method getContext,methylBaseDB-method getContext,methylDiff-method getContext,methylDiffDB-method getContext,methylRaw-method getContext,methylRawDB-method |
| get correlation between samples in methylBase or methylBaseDB object | getCorrelation getCorrelation,methylBase-method getCorrelation,methylBaseDB-method |
| get coverage stats from methylRaw object | getCoverageStats getCoverageStats,methylRaw-method getCoverageStats,methylRawDB-method |
| get the data slot from the methylKit objects | getData getData,methylBase-method getData,methylBaseDB-method getData,methylDiff-method getData,methylDiffDB-method getData,methylRaw-method getData,methylRawDB-method |
| Get path to database of the methylDB objects | getDBPath getDBPath,methylBaseDB-method getDBPath,methylDiffDB-method getDBPath,methylRawDB-method getDBPath,methylRawListDB-method |
| get Methylation stats from methylRaw or methylRawDB object | getMethylationStats getMethylationStats,methylRaw-method getMethylationStats,methylRawDB-method |
| get differentially methylated regions/bases based on cutoffs | getMethylDiff getMethylDiff,methylDiff-method getMethylDiff,methylDiffDB-method |
| Get or Set Sample-IDs of the methylKit objects | getSampleID getSampleID,methylBase-method getSampleID,methylBaseDB-method getSampleID,methylDiff-method getSampleID,methylDiffDB-method getSampleID,methylRaw-method getSampleID,methylRawDB-method getSampleID,methylRawList-method getSampleID,methylRawListDB-method getSampleID<- getSampleID<-,methylBase-method getSampleID<-,methylBaseDB-method getSampleID<-,methylDiff-method getSampleID<-,methylDiffDB-method getSampleID<-,methylRaw-method getSampleID<-,methylRawDB-method getSampleID<-,methylRawList-method getSampleID<-,methylRawListDB-method |
| Get or Set treatment vector of methylKit object | getTreatment getTreatment,getTreatment,methylDiffDB-method getTreatment,methylBase-method getTreatment,methylBaseDB-method getTreatment,methylDiff-method getTreatment,methylDiffDB-method getTreatment,methylRawList-method getTreatment,methylRawListDB-method getTreatment<- getTreatment<-,methylBase-method getTreatment<-,methylBaseDB-method getTreatment<-,methylDiff-method getTreatment<-,methylDiffDB-method getTreatment<-,methylRawList-method getTreatment<-,methylRawListDB-method |
| Join directly neighbouring segments produced by methSeg | joinSegmentNeighbours |
| coerce methylKit objects from memory to flat file database objects | makeMethylDB makeMethylDB,methylBase-method makeMethylDB,methylBase-methods makeMethylDB,methylDiff-method makeMethylDB,methylDiff-methods makeMethylDB,methylRaw-method makeMethylDB,methylRaw-methods makeMethylDB,methylRawList-method makeMethylDB,methylRawList-methods |
| read file(s) to methylRaw or methylRawList objects | methRead methRead,character,ANY,ANY-method methRead,character,character,character-method methRead,character-method methRead,list,ANY,ANY-method methRead,list,list,character-method |
| Segment methylation or differential methylation profile | methSeg |
| Export segments to BED files | methSeg2bed |
| An S4 class for methylation events sampled in multiple experiments | methylBase methylBase-class |
| Example methylBase object. | methylBase.obj |
| An S4 class for storing methylation events sampled in multiple experiments as flat file database | methylBaseDB methylBaseDB-class |
| An S4 class that holds differential methylation information | methylDiff methylDiff-class |
| Example methylKit objects. | methylDiff.obj |
| An S4 class that holds differential methylation information as flat file database | methylDiffDB methylDiffDB-class |
| Deprecated/Defunct functions | adjust.methylC annotate.WithFeature annotate.WithFeature.Flank annotate.WithGenicParts get.methylDiff getFeatsWithTargetsStats getFlanks getMembers getTargetAnnotationStats methylKit-defunct plotTargetAnnotation read read.bed read.bismark read.feature.flank read.transcript.features |
| An S4 class for holding raw methylation data from an alignment pipeline. | methylRaw methylRaw-class |
| An S4 class for storing raw methylation data as flat file database. | methylRawDB methylRawDB-class |
| An S4 class for holding a list of methylRaw objects. | methylRawList methylRawList-class |
| Example methylRawList object. | methylRawList.obj |
| An S4 class for holding a list of methylRawDB objects. | methylRawListDB methylRawListDB-class |
| normalize read coverage between samples | normalizeCoverage normalizeCoverage,methylRawList-method normalizeCoverage,methylRawListDB-method |
| Principal Components Analysis of Methylation data | PCASamples PCASamples,methylBase-method PCASamples,methylBaseDB-method |
| get percent methylation scores from methylBase or methylBaseDB object | percMethylation percMethylation,methylBase-method percMethylation,methylBaseDB-method |
| Pool replicates within groups to a single sample per group | pool pool,methylBase-method pool,methylBaseDB-method |
| Get methylation percentage from sorted Bismark alignments | processBismarkAln processBismarkAln,character,character,character-method processBismarkAln,list,list,character-method |
| load tabix file with header to methylDB | readMethylDB |
| Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix | reconstruct reconstruct,ANY,methylBase-method reconstruct,ANY,methylBaseDB-method reconstruct,methylBase-method reconstruct,methylBaseDB-method |
| Get regional counts for given GRanges or GRangesList object | regionCounts regionCounts,methylBase,GRanges-method regionCounts,methylBase,GRangesList-method regionCounts,methylBaseDB,GRanges-method regionCounts,methylBaseDB,GRangesList-method regionCounts,methylRaw,GRanges-method regionCounts,methylRaw,GRangesList-method regionCounts,methylRawDB,GRanges-method regionCounts,methylRawDB,GRangesList-method regionCounts,methylRawList,GRanges-method regionCounts,methylRawList,GRangesList-method regionCounts,methylRawListDB,GRanges-method regionCounts,methylRawListDB,GRangesList-method |
| Remove principal components from a methylBase object | removeComp removeComp,methylBase-method removeComp,methylBaseDB-method |
| Reorganize methylKit objects by creating new objects from subset of samples | reorganize reorganize,methylBase-method reorganize,methylBaseDB-method reorganize,methylRawList-method reorganize,methylRawListDB-method |
| selects rows from of methylKit objects | select select,methylBase-method select,methylBaseDB-method select,methylDiff-method select,methylDiffDB-method select,methylRaw-method select,methylRawDB-method |
| selects records of methylDB objects lying inside a GRanges range | selectByOverlap selectByOverlap,methylBase,GRanges-method selectByOverlap,methylBase-method selectByOverlap,methylBaseDB,GRanges-method selectByOverlap,methylBaseDB-method selectByOverlap,methylDiff,GRanges-method selectByOverlap,methylDiff-method selectByOverlap,methylDiffDB,GRanges-method selectByOverlap,methylDiffDB-method selectByOverlap,methylRaw,GRanges-method selectByOverlap,methylRaw-method selectByOverlap,methylRawDB,GRanges-method selectByOverlap,methylRawDB-method selectByOverlap,methylRawList,GRanges-method selectByOverlap,methylRawList-method selectByOverlap,methylRawListDB,GRanges-method selectByOverlap,methylRawListDB-method |
| show method for methylKit classes | show,methylBase show,methylBase-method show,methylBaseDB show,methylBaseDB-method show,methylDiff show,methylDiff-method show,methylDiffDB show,methylDiffDB-method show,methylRaw show,methylRaw-method show,methylRawDB show,methylRawDB-method show,methylRawList show,methylRawList-method show,methylRawListDB show,methylRawListDB-method |
| Get methylated/unmethylated base counts for tilling windows | tileMethylCounts tileMethylCounts,methylBase-method tileMethylCounts,methylBaseDB-method tileMethylCounts,methylRaw-method tileMethylCounts,methylRawDB-method tileMethylCounts,methylRawList-method tileMethylCounts,methylRawListDB-method |
| unite methylRawList to a single table | unite unite,methylRawList-method unite,methylRawListDB-method |
| update methylKit objects The method updates object from earlier versions (<v0.9.1) to latest object. | updateMethObject |
