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. Perl is needed to read SAM files only.

AuthorAltuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Gosdschan [aut]
Date of publicationNone
MaintainerAltuna Akalin <aakalin@gmail.com>
LicenseArtistic-2.0
Version1.0.0
http://code.google.com/p/methylkit/

View on Bioconductor

Man pages

adjustMethylC: Adjust measured 5mC levels using 5hmC levels

assocComp-methods: Associate principal components with sample annotations

bedgraph-methods: Get bedgraph from methylRaw, methylRawList and methylDiff...

calculateDiffMethDSS-methods: calculate Differential Methylation with DSS

calculateDiffMeth-methods: Calculate differential methylation statistics

clusterSamples-methods: Hierarchical Clustering using methylation data The function...

dataSim-methods: Simulate DNA methylation data

diffMethPerChr-methods: Get and plot the number of hyper/hypo methylated...

extract-methods: extract parts of...

filterByCoverage-methods: Filter methylRaw, methylRawDB, methylRawList and...

genomation-deprecated: Deprecated/Defunct functions

getAssembly-methods: get assembly of the genome

getContext-methods: get the context of methylation

getCorrelation-methods: get correlation between samples in methylBase or methylBaseDB...

getCoverageStats-methods: get coverage stats from methylRaw object

getData-methods: get the data slot from the methylKit objects

getDBPath-methods: Get path to database of the methylDB objects

getMethylationStats-methods: get Methylation stats from methylRaw or methylRawDB object

getMethylDiff-methods: get differentially methylated regions/bases based on cutoffs

getSampleID-methods: Get or Set Sample-IDs of the methylKit objects

getTreatment-methods: Get or Set treatment vector of methylKit object

makeMethylDB-methods: coerce methylKit objects from memory to flat file database...

methRead-methods: read file(s) to methylRaw or methylRawList objects

methSeg: Segment methylation or differential methylation profile

methSeg2bed: Export segments to BED files

methylBase-class: An S4 class for methylation events sampled in multiple...

methylBaseDB-class: An S4 class for storing methylation events sampled in...

methylBase.obj: Example methylBase object.

methylDiff-class: An S4 class that holds differential methylation information

methylDiffDB-class: An S4 class that holds differential methylation information...

methylDiff.obj: Example methylKit objects.

methylRaw-class: An S4 class for holding raw methylation data from an...

methylRawDB-class: An S4 class for storing raw methylation data as flat file...

methylRawList-class: An S4 class for holding a list of methylRaw objects.

methylRawListDB-class: An S4 class for holding a list of methylRawDB objects.

methylRawList.obj: Example methylRawList object.

normalizeCoverage-methods: normalize read coverage between samples

PCASamples-methods: Principal Components Analysis of Methylation data

percMethylation-methods: get percent methylation scores from methylBase or...

pool-methods: Pool replicates within groups to a single sample per group

processBismarkAln-methods: Get methylation percentage from sorted Bismark alignments

reconstruct-methods: Reconstruct methylBase or methylBaseDB object based on a new...

regionCounts: Get regional counts for given GRanges or GRangesList object

removeComp-methods: Remove principal components from a methylBase object

reorganize-methods: Reorganize methylKit objects by creating new objects from...

selectByOverlap-methods: selects records of methylDB objects lying inside a GRanges...

select-methods: selects rows from of methylKit objects

show-methods: show method for methylKit classes

tileMethylCounts-methods: Get methylated/unmethylated base counts for tilling windows

unite-methods: unite methylRawList to a single table

updateMethObject: update methylKit objects The method updates object from...

Functions

adjust.methylC Man page
adjustMethylC Man page
adjustMethylC,methylRawDB,methylRawDB-method Man page
adjustMethylC,methylRawListDB,methylRawListDB-method Man page
adjustMethylC,methylRawList,methylRawList-method Man page
adjustMethylC,methylRaw,methylRaw-method Man page
annotate.WithFeature Man page
annotate.WithFeature.Flank Man page
annotate.WithGenicParts Man page
assocComp Man page
bedgraph Man page
bedgraph,methylDiffDB-method Man page
bedgraph,methylDiff-method Man page
bedgraph,methylRawDB-method Man page
bedgraph,methylRawListDB-method Man page
bedgraph,methylRawList-method Man page
bedgraph,methylRaw-method Man page
calculateDiffMeth Man page
calculateDiffMethDSS Man page
calculateDiffMethDSS,methylBase-method Man page
calculateDiffMeth,methylBaseDB-method Man page
calculateDiffMeth,methylBase-method Man page
clusterSamples Man page
clusterSamples,methylBaseDB-method Man page
clusterSamples,methylBase-method Man page
dataSim Man page
diffMethPerChr Man page
diffMethPerChr,methylDiffDB-method Man page
diffMethPerChr,methylDiff-method Man page
extract Man page
filterByCoverage Man page
filterByCoverage,methylRawDB-method Man page
filterByCoverage,methylRawListDB-method Man page
filterByCoverage,methylRawList-method Man page
filterByCoverage,methylRaw-method Man page
genomation-deprecated Man page
getAssembly Man page
getAssembly,methylBaseDB-method Man page
getAssembly,methylBase-method Man page
getAssembly,methylDiffDB-method Man page
getAssembly,methylDiff-method Man page
getAssembly,methylRawDB-method Man page
getAssembly,methylRaw-method Man page
getContext Man page
getContext,methylBaseDB-method Man page
getContext,methylBase-method Man page
getContext,methylDiffDB-method Man page
getContext,methylDiff-method Man page
getContext,methylRawDB-method Man page
getContext,methylRaw-method Man page
getCorrelation Man page
getCorrelation,methylBaseDB-method Man page
getCorrelation,methylBase-method Man page
getCoverageStats Man page
getCoverageStats,methylRawDB-method Man page
getCoverageStats,methylRaw-method Man page
getData Man page
getData,methylBaseDB-method Man page
getData,methylBase-method Man page
getData,methylDiffDB-method Man page
getData,methylDiff-method Man page
getData,methylRawDB-method Man page
getData,methylRaw-method Man page
getDBPath Man page
getDBPath,methylBaseDB-method Man page
getDBPath,methylDiffDB-method Man page
getDBPath,methylRawDB-method Man page
getDBPath,methylRawListDB-method Man page
getFeatsWithTargetsStats Man page
getFlanks Man page
getMembers Man page
getMethylationStats Man page
getMethylationStats,methylRawDB-method Man page
getMethylationStats,methylRaw-method Man page
get.methylDiff Man page
getMethylDiff Man page
getMethylDiff,methylDiffDB-method Man page
getMethylDiff,methylDiff-method Man page
getSampleID Man page
getSampleID<- Man page
getSampleID<-,methylBaseDB-method Man page
getSampleID,methylBaseDB-method Man page
getSampleID<-,methylBase-method Man page
getSampleID,methylBase-method Man page
getSampleID<-,methylDiffDB-method Man page
getSampleID,methylDiffDB-method Man page
getSampleID<-,methylDiff-method Man page
getSampleID,methylDiff-method Man page
getSampleID<-,methylRawDB-method Man page
getSampleID,methylRawDB-method Man page
getSampleID<-,methylRawListDB-method Man page
getSampleID,methylRawListDB-method Man page
getSampleID<-,methylRawList-method Man page
getSampleID,methylRawList-method Man page
getSampleID<-,methylRaw-method Man page
getSampleID,methylRaw-method Man page
getTargetAnnotationStats Man page
getTreatment Man page
getTreatment<- Man page
getTreatment,getTreatment,methylDiffDB-method Man page
getTreatment<-,methylBaseDB-method Man page
getTreatment,methylBaseDB-method Man page
getTreatment<-,methylBase-method Man page
getTreatment,methylBase-method Man page
getTreatment<-,methylDiffDB-method Man page
getTreatment,methylDiffDB-method Man page
getTreatment<-,methylDiff-method Man page
getTreatment,methylDiff-method Man page
getTreatment<-,methylRawListDB-method Man page
getTreatment,methylRawListDB-method Man page
getTreatment<-,methylRawList-method Man page
getTreatment,methylRawList-method Man page
makeMethylDB Man page
makeMethylDB,methylBase-method Man page
makeMethylDB,methylBase-methods Man page
makeMethylDB,methylDiff-method Man page
makeMethylDB,methylDiff-methods Man page
makeMethylDB,methylRawList-method Man page
makeMethylDB,methylRawList-methods Man page
makeMethylDB,methylRaw-method Man page
makeMethylDB,methylRaw-methods Man page
methRead Man page
methRead,character,character,character-method Man page
methRead,list,list,character-method Man page
methSeg Man page
methSeg2bed Man page
methylBase Man page
[,methylBase,ANY,ANY,ANY-method Man page
[,methylBase,ANY,ANY-method Man page
methylBase-class Man page
methylBaseDB Man page
[,methylBaseDB,ANY,ANY,ANY-method Man page
[,methylBaseDB,ANY,ANY-method Man page
methylBaseDB-class Man page
methylBase.obj Man page
methylDiff Man page
[,methylDiff,ANY,ANY,ANY-method Man page
[,methylDiff,ANY,ANY-method Man page
methylDiff-class Man page
methylDiffDB Man page
[,methylDiffDB,ANY,ANY,ANY-method Man page
[,methylDiffDB,ANY,ANY-method Man page
methylDiffDB-class Man page
methylDiff.obj Man page
methylRaw Man page
[,methylRaw,ANY,ANY,ANY-method Man page
[,methylRaw,ANY,ANY-method Man page
methylRaw-class Man page
methylRawDB Man page
[,methylRawDB,ANY,ANY,ANY-method Man page
[,methylRawDB,ANY,ANY-method Man page
methylRawDB-class Man page
methylRawList Man page
methylRawList-class Man page
methylRawListDB Man page
methylRawListDB-class Man page
methylRawList.obj Man page
normalizeCoverage Man page
normalizeCoverage,methylRawListDB-method Man page
normalizeCoverage,methylRawList-method Man page
PCASamples Man page
PCASamples,methylBaseDB-method Man page
PCASamples,methylBase-method Man page
percMethylation Man page
percMethylation,methylBaseDB-method Man page
percMethylation,methylBase-method Man page
plotTargetAnnotation Man page
pool Man page
pool,methylBaseDB-method Man page
pool,methylBase-method Man page
processBismarkAln Man page
processBismarkAln,character,character,character-method Man page
processBismarkAln,list,list,character-method Man page
read Man page
read.bed Man page
read.bismark Man page
read.feature.flank Man page
read.transcript.features Man page
reconstruct Man page
reconstruct,ANY,methylBaseDB-method Man page
reconstruct,ANY,methylBase-method Man page
reconstruct,methylBaseDB-method Man page
reconstruct,methylBase-method Man page
regionCounts Man page
regionCounts,methylBaseDB,GRangesList-method Man page
regionCounts,methylBaseDB,GRanges-method Man page
regionCounts,methylBase,GRangesList-method Man page
regionCounts,methylBase,GRanges-method Man page
regionCounts,methylRawDB,GRangesList-method Man page
regionCounts,methylRawDB,GRanges-method Man page
regionCounts,methylRaw,GRangesList-method Man page
regionCounts,methylRaw,GRanges-method Man page
regionCounts,methylRawListDB,GRangesList-method Man page
regionCounts,methylRawListDB,GRanges-method Man page
regionCounts,methylRawList,GRangesList-method Man page
regionCounts,methylRawList,GRanges-method Man page
removeComp Man page
removeComp,methylBaseDB-method Man page
removeComp,methylBase-method Man page
reorganize Man page
reorganize,methylBaseDB-method Man page
reorganize,methylBase-method Man page
reorganize,methylRawListDB-method Man page
reorganize,methylRawList-method Man page
select Man page
selectByOverlap Man page
selectByOverlap,methylBaseDB-method Man page
selectByOverlap,methylBase-method Man page
selectByOverlap,methylDiffDB-method Man page
selectByOverlap,methylDiff-method Man page
selectByOverlap,methylRawDB-method Man page
selectByOverlap,methylRawListDB-method Man page
selectByOverlap,methylRawList-method Man page
selectByOverlap,methylRaw-method Man page
select,methylBaseDB-method Man page
select,methylBase-method Man page
select,methylDiffDB-method Man page
select,methylDiff-method Man page
select,methylRawDB-method Man page
select,methylRaw-method Man page
show,methylBase Man page
show,methylBaseDB Man page
show,methylBaseDB-method Man page
show,methylBase-method Man page
show,methylDiff Man page
show,methylDiffDB Man page
show,methylDiffDB-method Man page
show,methylDiff-method Man page
show,methylRaw Man page
show,methylRawDB Man page
show,methylRawDB-method Man page
show,methylRawList Man page
show,methylRawListDB Man page
show,methylRawListDB-method Man page
show,methylRawList-method Man page
show,methylRaw-method Man page
tileMethylCounts Man page
tileMethylCounts,methylBaseDB-method Man page
tileMethylCounts,methylBase-method Man page
tileMethylCounts,methylRawDB-method Man page
tileMethylCounts,methylRawListDB-method Man page
tileMethylCounts,methylRawList-method Man page
tileMethylCounts,methylRaw-method Man page
unite Man page
unite,methylRawListDB-method Man page
unite,methylRawList-method Man page
updateMethObject Man page

Files

methylKit/.Rinstignore
methylKit/DESCRIPTION
methylKit/NAMESPACE
methylKit/NEWS
methylKit/R
methylKit/R/RcppExports.R methylKit/R/adjust.methylC.R methylKit/R/backbone.R methylKit/R/batchControl.R methylKit/R/bedgraph.R methylKit/R/clusterSamples.R methylKit/R/dataSim.R methylKit/R/deprecated_defunct.R methylKit/R/diffMeth.R methylKit/R/diffMethDSS.R methylKit/R/document_data.R methylKit/R/methSeg.R methylKit/R/methylDBClasses.R methylKit/R/methylDBFunctions.R methylKit/R/methylKit.R methylKit/R/normalizeCoverage.R methylKit/R/percMethylation.R methylKit/R/pool.R methylKit/R/processBismarkAln.R methylKit/R/regionalize.R methylKit/R/reorganize.R methylKit/R/tabix.functions.R methylKit/R/updateMethObject.R
methylKit/README.md
methylKit/build
methylKit/build/vignette.rds
methylKit/data
methylKit/data/methylKit.RData
methylKit/inst
methylKit/inst/CITATION
methylKit/inst/doc
methylKit/inst/doc/methylKit.R
methylKit/inst/doc/methylKit.Rmd
methylKit/inst/doc/methylKit.html
methylKit/inst/extdata
methylKit/inst/extdata/control1.myCpG.txt
methylKit/inst/extdata/control2.myCpG.txt
methylKit/inst/extdata/cpgi.hg18.bed.txt
methylKit/inst/extdata/ctrl1.txt.bgz
methylKit/inst/extdata/ctrl2.txt.bgz
methylKit/inst/extdata/generic1.CpG.txt
methylKit/inst/extdata/refseq.hg18.bed.txt
methylKit/inst/extdata/test.fastq_bismark.sorted.min.sam
methylKit/inst/extdata/test.fastq_bismark.unsorted.min.sam
methylKit/inst/extdata/test1.myCpG.txt
methylKit/inst/extdata/test1.txt.bgz
methylKit/inst/extdata/test1_test2_ctrl1_ctrl2.txt.bgz
methylKit/inst/extdata/test1_test2_ctrl1_ctrl2_diffMeth.txt.bgz
methylKit/inst/extdata/test2.myCpG.txt
methylKit/inst/extdata/test2.txt.bgz
methylKit/inst/scripts
methylKit/inst/scripts/create.data.R
methylKit/man
methylKit/man/PCASamples-methods.Rd methylKit/man/adjustMethylC.Rd methylKit/man/assocComp-methods.Rd methylKit/man/bedgraph-methods.Rd methylKit/man/calculateDiffMeth-methods.Rd methylKit/man/calculateDiffMethDSS-methods.Rd methylKit/man/clusterSamples-methods.Rd methylKit/man/dataSim-methods.Rd methylKit/man/diffMethPerChr-methods.Rd methylKit/man/extract-methods.Rd methylKit/man/filterByCoverage-methods.Rd methylKit/man/genomation-deprecated.Rd methylKit/man/getAssembly-methods.Rd methylKit/man/getContext-methods.Rd methylKit/man/getCorrelation-methods.Rd methylKit/man/getCoverageStats-methods.Rd methylKit/man/getDBPath-methods.Rd methylKit/man/getData-methods.Rd methylKit/man/getMethylDiff-methods.Rd methylKit/man/getMethylationStats-methods.Rd methylKit/man/getSampleID-methods.Rd methylKit/man/getTreatment-methods.Rd methylKit/man/makeMethylDB-methods.Rd methylKit/man/methRead-methods.Rd methylKit/man/methSeg.Rd methylKit/man/methSeg2bed.Rd methylKit/man/methylBase-class.Rd methylKit/man/methylBase.obj.Rd methylKit/man/methylBaseDB-class.Rd methylKit/man/methylDiff-class.Rd methylKit/man/methylDiff.obj.Rd methylKit/man/methylDiffDB-class.Rd methylKit/man/methylRaw-class.Rd methylKit/man/methylRawDB-class.Rd methylKit/man/methylRawList-class.Rd methylKit/man/methylRawList.obj.Rd methylKit/man/methylRawListDB-class.Rd methylKit/man/normalizeCoverage-methods.Rd methylKit/man/percMethylation-methods.Rd methylKit/man/pool-methods.Rd methylKit/man/processBismarkAln-methods.Rd methylKit/man/reconstruct-methods.Rd methylKit/man/regionCounts.Rd methylKit/man/removeComp-methods.Rd methylKit/man/reorganize-methods.Rd methylKit/man/select-methods.Rd methylKit/man/selectByOverlap-methods.Rd methylKit/man/show-methods.Rd methylKit/man/tileMethylCounts-methods.Rd methylKit/man/unite-methods.Rd methylKit/man/updateMethObject.Rd
methylKit/src
methylKit/src/Makevars
methylKit/src/Makevars.win
methylKit/src/RcppExports.cpp
methylKit/src/methCall.cpp
methylKit/tests
methylKit/tests/testthat
methylKit/tests/testthat.R
methylKit/tests/testthat/test-1-read.r
methylKit/tests/testthat/test-2-unite.r
methylKit/tests/testthat/test-3-clusterSamples.r
methylKit/tests/testthat/test-4-calculateDiffMeth.r
methylKit/tests/testthat/test-5-read.bismark.r
methylKit/tests/testthat/test-6-regionCounts.r
methylKit/tests/testthat/test-7-dataSim.r
methylKit/tests/testthat/test-8-calculateDiffMethDSS.r
methylKit/tests/testthat/test-8-methSeg.r
methylKit/tests/testthat/test-9-tidyUp.r
methylKit/vignettes
methylKit/vignettes/Sweavel.sty
methylKit/vignettes/Vignette_methylKit.bib
methylKit/vignettes/methylKit.Rmd

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Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.