Man pages for al2na/methylKit
DNA methylation analysis from high-throughput bisulfite sequencing results
| 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... |
| 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 |
| joinSegmentNeighbours | Join directly neighbouring segments produced by methSeg |
| 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. |
| methylKit-defunct | Deprecated/Defunct functions |
| 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 |
| readMethylDB-methods | load tabix file with header to methylDB |
| 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... |
