DNA methylation analysis from high-throughput bisulfite
sequencing results
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Documentation for package ‘methylKit’ version 1.24.0
Help Pages
A B C D E F G J M N P R S T U misc
-- A --
| adjust.methylC | Deprecated/Defunct functions |
| 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 |
| extract-method | 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 --
| get.methylDiff | Deprecated/Defunct functions |
| 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 |
-- J --
| joinSegmentNeighbours | Join directly neighbouring segments produced by methSeg |
-- 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 |
| methylKit-defunct | Deprecated/Defunct functions |
| 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 | Deprecated/Defunct functions |
| read.bed | Deprecated/Defunct functions |
| read.bismark | Deprecated/Defunct functions |
| read.feature.flank | Deprecated/Defunct functions |
| read.transcript.features | Deprecated/Defunct functions |
| readMethylDB | load tabix file with header to methylDB |
| 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 |