methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results
Version 1.2.0

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.

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AuthorAltuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Gosdschan [aut]
Bioconductor views DNAMethylation MethylSeq Sequencing
Date of publicationNone
MaintainerAltuna Akalin <aakalin@gmail.com>
LicenseArtistic-2.0
Version1.2.0
URL http://code.google.com/p/methylkit/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methylKit")

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

CpG.dinuc.unify Source code
CpG.dinuc.unifyOld Source code
PCASamples Man page
PCASamples,methylBase-method Man page
PCASamples,methylBaseDB-method Man page
QValuesfun Source code
SLIMfunc Source code
[,methylBase,ANY,ANY,ANY-method Man page
[,methylBase,ANY,ANY-method Man page
[,methylBaseDB,ANY,ANY,ANY-method Man page
[,methylBaseDB,ANY,ANY-method Man page
[,methylDiff,ANY,ANY,ANY-method Man page
[,methylDiff,ANY,ANY-method Man page
[,methylDiffDB,ANY,ANY,ANY-method Man page
[,methylDiffDB,ANY,ANY-method Man page
[,methylRaw,ANY,ANY,ANY-method Man page
[,methylRaw,ANY,ANY-method Man page
[,methylRawDB,ANY,ANY,ANY-method Man page
[,methylRawDB,ANY,ANY-method Man page
adjlim Source code
adjust.methylC Man page Source code
adjustMethylC Man page
adjustMethylC,methylRaw,methylRaw-method Man page
adjustMethylC,methylRawDB,methylRawDB-method Man page
adjustMethylC,methylRawList,methylRawList-method Man page
adjustMethylC,methylRawListDB,methylRawListDB-method Man page
annotate.WithFeature Man page Source code
annotate.WithFeature.Flank Man page Source code
annotate.WithGenicParts Man page Source code
applyTbxByChr Source code
applyTbxByChunk Source code
applyTbxByOverlap Source code
assocComp Man page Source code
bedgraph Man page
bedgraph,methylDiff-method Man page
bedgraph,methylDiffDB-method Man page
bedgraph,methylRaw-method Man page
bedgraph,methylRawDB-method Man page
bedgraph,methylRawList-method Man page
bedgraph,methylRawListDB-method Man page
calculateDiffMeth Man page
calculateDiffMeth,methylBase-method Man page
calculateDiffMeth,methylBaseDB-method Man page
calculateDiffMethDSS Man page
calculateDiffMethDSS,methylBase-method Man page
callDML2 Source code
catsub2tabix Source code
check.dbdir Source code
check.pipeline.list Source code
cluster Source code
clusterSamples Man page
clusterSamples,methylBase-method Man page
clusterSamples,methylBaseDB-method Man page
colSds Source code
compute.mean Source code
compute.waldStat Source code
dataSim Man page Source code
dbb Source code
densityFind Source code
df2tabix Source code
diagPlot Source code
diffMethPerChr Man page
diffMethPerChr,methylDiff-method Man page
diffMethPerChr,methylDiffDB-method Man page
dispersion.shrinkage Source code
dist.cor Source code
est.prior.logN Source code
estimatePhi Source code
estimateShrinkageMN Source code
extract Man page
f1 Source code
fast.fisher Source code
filterByCoverage Man page
filterByCoverage,methylRaw-method Man page
filterByCoverage,methylRawDB-method Man page
filterByCoverage,methylRawList-method Man page
filterByCoverage,methylRawListDB-method Man page
fread.gzipped Source code
genomation-deprecated Man page
get.methylDiff Man page Source code
getAssembly Man page
getAssembly,methylBase-method Man page
getAssembly,methylBaseDB-method Man page
getAssembly,methylDiff-method Man page
getAssembly,methylDiffDB-method Man page
getAssembly,methylRaw-method Man page
getAssembly,methylRawDB-method Man page
getContext Man page
getContext,methylBase-method Man page
getContext,methylBaseDB-method Man page
getContext,methylDiff-method Man page
getContext,methylDiffDB-method Man page
getContext,methylRaw-method Man page
getContext,methylRawDB-method Man page
getCorrelation Man page
getCorrelation,methylBase-method Man page
getCorrelation,methylBaseDB-method Man page
getCoverageStats Man page
getCoverageStats,methylRaw-method Man page
getCoverageStats,methylRawDB-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
getData Man page
getData,methylBase-method Man page
getData,methylBaseDB-method Man page
getData,methylDiff-method Man page
getData,methylDiffDB-method Man page
getData,methylRaw-method Man page
getData,methylRawDB-method Man page
getFeatsWithTargetsStats Man page Source code
getFlanks Man page Source code
getMembers Man page Source code
getMethylDiff Man page
getMethylDiff,methylDiff-method Man page
getMethylDiff,methylDiffDB-method Man page
getMethylationStats Man page
getMethylationStats,methylRaw-method Man page
getMethylationStats,methylRawDB-method Man page
getSampleID Man page
getSampleID,methylBase-method Man page Man page
getSampleID,methylBaseDB-method Man page Man page
getSampleID,methylDiff-method Man page Man page
getSampleID,methylDiffDB-method Man page Man page
getSampleID,methylRaw-method Man page Man page
getSampleID,methylRawDB-method Man page Man page
getSampleID,methylRawList-method Man page Man page
getSampleID,methylRawListDB-method Man page Man page
getSampleID<- Man page
getSampleID<-,methylBase-method Man page
getSampleID<-,methylBaseDB-method Man page
getSampleID<-,methylDiff-method Man page
getSampleID<-,methylDiffDB-method Man page
getSampleID<-,methylRaw-method Man page
getSampleID<-,methylRawDB-method Man page
getSampleID<-,methylRawList-method Man page
getSampleID<-,methylRawListDB-method Man page
getTabixByChr Source code
getTabixByChunk Source code
getTabixByOverlap Source code
getTargetAnnotationStats Man page Source code
getTreatment Man page
getTreatment,getTreatment,methylDiffDB-method Man page
getTreatment,methylBase-method Man page Man page
getTreatment,methylBaseDB-method Man page Man page
getTreatment,methylDiff-method Man page Man page
getTreatment,methylDiffDB-method Man page
getTreatment,methylRawList-method Man page Man page
getTreatment,methylRawListDB-method Man page Man page
getTreatment<- Man page
getTreatment<-,methylBase-method Man page
getTreatment<-,methylBaseDB-method Man page
getTreatment<-,methylDiff-method Man page
getTreatment<-,methylDiffDB-method Man page
getTreatment<-,methylRawList-method Man page
getTreatment<-,methylRawListDB-method Man page
headTabix Source code
influence Source code
logReg Source code
makeMethTabix Source code
makeMethylBaseDB Source code
makeMethylDB Man page
makeMethylDB,methylBase-method Man page
makeMethylDB,methylBase-methods Man page
makeMethylDB,methylDiff-method Man page
makeMethylDB,methylDiff-methods Man page
makeMethylDB,methylRaw-method Man page
makeMethylDB,methylRaw-methods Man page
makeMethylDB,methylRawList-method Man page
makeMethylDB,methylRawList-methods Man page
makeMethylDiffDB Source code
makeMethylRawDB Source code
mergeData.counts Source code
mergeTabix Source code
mergeTbxByChr Source code
methCall Source code
methRead Man page
methRead,character,character,character-method Man page
methRead,list,list,character-method Man page
methSeg Man page Source code Source code
methSeg2bed Man page Source code
methylBase Man page
methylBase-class Man page
methylBase.obj Man page
methylBaseDB Man page
methylBaseDB-class Man page
methylDiff Man page
methylDiff-class Man page
methylDiff.obj Man page
methylDiffDB Man page
methylDiffDB-class Man page
methylRaw Man page
methylRaw-class Man page
methylRawDB Man page
methylRawDB-class Man page
methylRawList Man page
methylRawList-class Man page
methylRawList.obj Man page
methylRawListDB Man page
methylRawListDB-class Man page
normalizeCoverage Man page
normalizeCoverage,methylRawList-method Man page
normalizeCoverage,methylRawListDB-method Man page
onUnload Source code
p.adjusted Source code Source code
pcaPlot Source code
pcaPlotT Source code
percMethylation Man page
percMethylation,methylBase-method Man page
percMethylation,methylBaseDB-method Man page
plotTargetAnnotation Man page Source code
pool Man page
pool,methylBase-method Man page
pool,methylBaseDB-method Man page
procBismarkCoverage Source code
procBismarkCytosineReport Source code
processBismarkAln Man page
processBismarkAln,character,character,character-method Man page
processBismarkAln,list,list,character-method Man page
read Man page Source code
read.bed Man page Source code
read.bismark Man page Source code
read.feature.flank Man page Source code
read.transcript.features Man page Source code
readMethylBaseDB Source code
readMethylDiffDB Source code
readMethylRawDB Source code
readTableFast Source code
reconstruct Man page
reconstruct,ANY,methylBase-method Man page
reconstruct,ANY,methylBaseDB-method Man page
reconstruct,methylBase-method Man page
reconstruct,methylBaseDB-method Man page
regionCounts Man page
regionCounts,methylBase,GRanges-method Man page
regionCounts,methylBase,GRangesList-method Man page
regionCounts,methylBaseDB,GRanges-method Man page
regionCounts,methylBaseDB,GRangesList-method Man page
regionCounts,methylRaw,GRanges-method Man page
regionCounts,methylRaw,GRangesList-method Man page
regionCounts,methylRawDB,GRanges-method Man page
regionCounts,methylRawDB,GRangesList-method Man page
regionCounts,methylRawList,GRanges-method Man page
regionCounts,methylRawList,GRangesList-method Man page
regionCounts,methylRawListDB,GRanges-method Man page
regionCounts,methylRawListDB,GRangesList-method Man page
removeComp Man page
removeComp,methylBase-method Man page
removeComp,methylBaseDB-method Man page
reorganize Man page
reorganize,methylBase-method Man page
reorganize,methylBaseDB-method Man page
reorganize,methylRawList-method Man page
reorganize,methylRawListDB-method Man page
rowSds Source code
rowVars Source code
select Man page
select,methylBase-method Man page
select,methylBaseDB-method Man page
select,methylDiff-method Man page
select,methylDiffDB-method Man page
select,methylRaw-method Man page
select,methylRawDB-method Man page
selectByOverlap Man page
selectByOverlap,methylBase-method Man page
selectByOverlap,methylBaseDB-method Man page
selectByOverlap,methylDiff-method Man page
selectByOverlap,methylDiffDB-method Man page
selectByOverlap,methylRaw-method Man page
selectByOverlap,methylRawDB-method Man page
selectByOverlap,methylRawList-method Man page
selectByOverlap,methylRawListDB-method Man page
setMethylDBNames Source code
show,methylBase Man page
show,methylBase-method Man page
show,methylBaseDB Man page
show,methylBaseDB-method Man page
show,methylDiff Man page
show,methylDiff-method Man page
show,methylDiffDB Man page
show,methylDiffDB-method Man page
show,methylRaw Man page
show,methylRaw-method Man page
show,methylRawDB Man page
show,methylRawDB-method Man page
show,methylRawList Man page
show,methylRawList-method Man page
show,methylRawListDB Man page
show,methylRawListDB-method Man page
sortPos Source code
structureAMPoutput Source code
structureGeneric Source code
tabix2df Source code
tabix2dt Source code
tabix2gr Source code
tileMethylCounts Man page
tileMethylCounts,methylBase-method Man page
tileMethylCounts,methylBaseDB-method Man page
tileMethylCounts,methylRaw-method Man page
tileMethylCounts,methylRawDB-method Man page
tileMethylCounts,methylRawList-method Man page
tileMethylCounts,methylRawListDB-method Man page
unite Man page
unite,methylRawList-method Man page
unite,methylRawListDB-method Man page
updateMethObject Man page
valid.methylBaseDB Source code
valid.methylDiffDB Source code
valid.methylRawDB Source code
valid.methylRawListDB Source code
valid.methylRawObj Source code
waldTest.DML Source code
write.bed Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/adjust.methylC.R
R/backbone.R
R/batchControl.R
R/bedgraph.R
R/clusterSamples.R
R/dataSim.R
R/deprecated_defunct.R
R/diffMeth.R
R/diffMethDSS.R
R/document_data.R
R/methSeg.R
R/methylDBClasses.R
R/methylDBFunctions.R
R/methylKit.R
R/normalizeCoverage.R
R/onUnload.R
R/percMethylation.R
R/pool.R
R/processBismarkAln.R
R/regionalize.R
R/reorganize.R
R/tabix.functions.R
R/updateMethObject.R
README.md
build
build/vignette.rds
data
data/methylKit.RData
inst
inst/CITATION
inst/doc
inst/doc/methylKit.R
inst/doc/methylKit.Rmd
inst/doc/methylKit.html
inst/extdata
inst/extdata/control1.myCpG.txt
inst/extdata/control2.myCpG.txt
inst/extdata/cpgi.hg18.bed.txt
inst/extdata/ctrl.bismark_paired_end.sorted.bam
inst/extdata/ctrl.bismark_paired_end.sorted.wh.sam
inst/extdata/ctrl1.txt.bgz
inst/extdata/ctrl2.txt.bgz
inst/extdata/generic1.CpG.txt
inst/extdata/refseq.hg18.bed.txt
inst/extdata/test.bismark_single_end.sorted.bam
inst/extdata/test.bismark_single_end.sorted.wh.sam
inst/extdata/test.fastq_bismark.sorted.min.sam
inst/extdata/test.fastq_bismark.unsorted.min.sam
inst/extdata/test1.myCpG.txt
inst/extdata/test1.txt.bgz
inst/extdata/test1_test2_ctrl1_ctrl2.txt.bgz
inst/extdata/test1_test2_ctrl1_ctrl2_diffMeth.txt.bgz
inst/extdata/test2.myCpG.txt
inst/extdata/test2.txt.bgz
inst/scripts
inst/scripts/create.data.R
man
man/PCASamples-methods.Rd
man/adjustMethylC.Rd
man/assocComp-methods.Rd
man/bedgraph-methods.Rd
man/calculateDiffMeth-methods.Rd
man/calculateDiffMethDSS-methods.Rd
man/clusterSamples-methods.Rd
man/dataSim-methods.Rd
man/diffMethPerChr-methods.Rd
man/extract-methods.Rd
man/filterByCoverage-methods.Rd
man/genomation-deprecated.Rd
man/getAssembly-methods.Rd
man/getContext-methods.Rd
man/getCorrelation-methods.Rd
man/getCoverageStats-methods.Rd
man/getDBPath-methods.Rd
man/getData-methods.Rd
man/getMethylDiff-methods.Rd
man/getMethylationStats-methods.Rd
man/getSampleID-methods.Rd
man/getTreatment-methods.Rd
man/makeMethylDB-methods.Rd
man/methRead-methods.Rd
man/methSeg.Rd
man/methSeg2bed.Rd
man/methylBase-class.Rd
man/methylBase.obj.Rd
man/methylBaseDB-class.Rd
man/methylDiff-class.Rd
man/methylDiff.obj.Rd
man/methylDiffDB-class.Rd
man/methylRaw-class.Rd
man/methylRawDB-class.Rd
man/methylRawList-class.Rd
man/methylRawList.obj.Rd
man/methylRawListDB-class.Rd
man/normalizeCoverage-methods.Rd
man/percMethylation-methods.Rd
man/pool-methods.Rd
man/processBismarkAln-methods.Rd
man/reconstruct-methods.Rd
man/regionCounts.Rd
man/removeComp-methods.Rd
man/reorganize-methods.Rd
man/select-methods.Rd
man/selectByOverlap-methods.Rd
man/show-methods.Rd
man/tileMethylCounts-methods.Rd
man/unite-methods.Rd
man/updateMethObject.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/methCall.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test-1-read.r
tests/testthat/test-10-readTabix.r
tests/testthat/test-11-pool.r
tests/testthat/test-2-unite.r
tests/testthat/test-3-clusterSamples.r
tests/testthat/test-4-calculateDiffMeth.r
tests/testthat/test-5-processBismarkAln.r
tests/testthat/test-6-regionCounts.r
tests/testthat/test-7-dataSim.r
tests/testthat/test-8-calculateDiffMethDSS.r
tests/testthat/test-8-methSeg.r
tests/testthat/test-999-tidyUp.r
vignettes
vignettes/Sweavel.sty
vignettes/Vignette_methylKit.bib
vignettes/methylKit.Rmd
methylKit documentation built on May 20, 2017, 9:30 p.m.