# DNA methylation analysis from high-throughput bisulfite sequencing results

## Documentation for package ‘methylKit’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G M N P R S T U misc

## -- A --

adjust.methylC | Adjust measured 5mC levels using 5hmC levels
adjustMethylC | Adjust measured 5mC levels using 5hmC levels
adjustMethylC-method | Adjust measured 5mC levels using 5hmC levels
annotate.WithFeature | Deprecated/Defunct functions
annotate.WithFeature.Flank | Deprecated/Defunct functions
annotate.WithGenicParts | Deprecated/Defunct functions
assocComp | Associate principal components with sample annotations

## -- B --

bedgraph | Get bedgraph from methylRaw, methylRawList and methylDiff objects
bedgraph-method | Get bedgraph from methylRaw, methylRawList and methylDiff objects

## -- C --

calculateDiffMeth | Calculate differential methylation statistics
calculateDiffMeth-method | Calculate differential methylation statistics
calculateDiffMethDSS | calculate Differential Methylation with DSS
calculateDiffMethDSS-method | calculate Differential Methylation with DSS
clusterSamples | 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-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.

## -- D --

dataSim | Simulate DNA methylation data
diffMethPerChr | Get and plot the number of hyper/hypo methylated regions/bases per chromosome
diffMethPerChr-method | Get and plot the number of hyper/hypo methylated regions/bases per chromosome

## -- E --

extract | extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data

## -- F --

filterByCoverage | Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage
filterByCoverage-method | Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage

## -- G --

genomation-deprecated | Deprecated/Defunct functions
get.methylDiff | get differentially methylated regions/bases based on cutoffs
getAssembly | get assembly of the genome
getAssembly-method | get assembly of the genome
getContext | get the context of methylation
getContext-method | get the context of methylation
getCorrelation | get correlation between samples in methylBase or methylBaseDB object
getCorrelation-method | get correlation between samples in methylBase or methylBaseDB object
getCoverageStats | get coverage stats from methylRaw object
getCoverageStats-method | get coverage stats from methylRaw object
getData | get the data slot from the methylKit objects
getData-method | get the data slot from the methylKit objects
getDBPath | Get path to database of the methylDB objects
getDBPath-method | Get path to database of the methylDB objects
getFeatsWithTargetsStats | Deprecated/Defunct functions
getFlanks | Deprecated/Defunct functions
getMembers | Deprecated/Defunct functions
getMethylationStats | get Methylation stats from methylRaw or methylRawDB object
getMethylationStats-method | get Methylation stats from methylRaw or methylRawDB object
getMethylDiff | get differentially methylated regions/bases based on cutoffs
getMethylDiff-method | get differentially methylated regions/bases based on cutoffs
getSampleID | Get or Set Sample-IDs of the methylKit objects
getSampleID-method | Get or Set Sample-IDs of the methylKit objects
getSampleID<- | Get or Set Sample-IDs of the methylKit objects
getSampleID<--method | Get or Set Sample-IDs of the methylKit objects
getTargetAnnotationStats | Deprecated/Defunct functions
getTreatment | Get or Set treatment vector of methylKit object
getTreatment-method | Get or Set treatment vector of methylKit object
getTreatment<- | Get or Set treatment vector of methylKit object
getTreatment<--method | Get or Set treatment vector of methylKit object

## -- M --

makeMethylDB | coerce methylKit objects from memory to flat file database objects
makeMethylDB,methylBase-methods | coerce methylKit objects from memory to flat file database objects
makeMethylDB,methylDiff-methods | coerce methylKit objects from memory to flat file database objects
makeMethylDB,methylRaw-methods | coerce methylKit objects from memory to flat file database objects
makeMethylDB,methylRawList-methods | coerce methylKit objects from memory to flat file database objects
makeMethylDB-method | coerce methylKit objects from memory to flat file database objects
methRead | read file(s) to methylRaw or methylRawList objects
methRead-method | read file(s) to methylRaw or methylRawList objects
methSeg | Segment methylation or differential methylation profile
methSeg2bed | Export segments to BED files
methylBase | An S4 class for methylation events sampled in multiple experiments
methylBase-class | An S4 class for methylation events sampled in multiple experiments
methylBase.obj | Example methylBase object.
methylBaseDB | An S4 class for storing methylation events sampled in multiple experiments as flat file database
methylBaseDB-class | An S4 class for storing methylation events sampled in multiple experiments as flat file database
methylDiff | An S4 class that holds differential methylation information
methylDiff-class | An S4 class that holds differential methylation information
methylDiff.obj | Example methylKit objects.
methylDiffDB | An S4 class that holds differential methylation information as flat file database
methylDiffDB-class | An S4 class that holds differential methylation information as flat file database
methylRaw | An S4 class for holding raw methylation data from an alignment pipeline.
methylRaw-class | An S4 class for holding raw methylation data from an alignment pipeline.
methylRawDB | An S4 class for storing raw methylation data as flat file database.
methylRawDB-class | An S4 class for storing raw methylation data as flat file database.
methylRawList | An S4 class for holding a list of methylRaw objects.
methylRawList-class | An S4 class for holding a list of methylRaw objects.
methylRawList.obj | Example methylRawList object.
methylRawListDB | An S4 class for holding a list of methylRawDB objects.
methylRawListDB-class | An S4 class for holding a list of methylRawDB objects.

## -- N --

normalizeCoverage | normalize read coverage between samples
normalizeCoverage-method | normalize read coverage between samples

## -- P --

PCASamples | Principal Components Analysis of Methylation data
PCASamples-method | Principal Components Analysis of Methylation data
percMethylation | get percent methylation scores from methylBase or methylBaseDB object
percMethylation-method | get percent methylation scores from methylBase or methylBaseDB object
plotTargetAnnotation | Deprecated/Defunct functions
pool | Pool replicates within groups to a single sample per group
pool-method | Pool replicates within groups to a single sample per group
processBismarkAln | Get methylation percentage from sorted Bismark alignments
processBismarkAln-method | Get methylation percentage from sorted Bismark alignments

## -- R --

read | read file(s) to methylRaw or methylRawList objects
read.bed | Deprecated/Defunct functions
read.bismark | Get methylation percentage from sorted Bismark alignments
read.feature.flank | Deprecated/Defunct functions
read.transcript.features | Deprecated/Defunct functions
reconstruct | Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix
reconstruct-method | Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix
regionCounts | Get regional counts for given GRanges or GRangesList object
regionCounts-method | Get regional counts for given GRanges or GRangesList object
removeComp | Remove principal components from a methylBase object
removeComp-method | Remove principal components from a methylBase object
reorganize | Reorganize methylKit objects by creating new objects from subset of samples
reorganize-method | Reorganize methylKit objects by creating new objects from subset of samples

## -- S --

select | selects rows from of methylKit objects
select-method | selects rows from of methylKit objects
selectByOverlap | selects records of methylDB objects lying inside a GRanges range
selectByOverlap-method | selects records of methylDB objects lying inside a GRanges range
show,methylBase | show method for methylKit classes
show,methylBaseDB | show method for methylKit classes
show,methylDiff | show method for methylKit classes
show,methylDiffDB | show method for methylKit classes
show,methylRaw | show method for methylKit classes
show,methylRawDB | show method for methylKit classes
show,methylRawList | show method for methylKit classes
show,methylRawListDB | show method for methylKit classes
show-method | show method for methylKit classes

## -- T --

tileMethylCounts | Get methylated/unmethylated base counts for tilling windows
tileMethylCounts-method | Get methylated/unmethylated base counts for tilling windows

## -- U --

unite | unite methylRawList to a single table
unite-method | unite methylRawList to a single table
updateMethObject | update methylKit objects The method updates object from earlier versions (<v0.9.1) to latest object.

## -- misc --

[-method | extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data