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A B C D E F G M N P R S T U misc
| 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 | Annotate object with a set of genomic features |
| annotate.WithFeature.Flank | Annotate an object with two sets of genomic features |
| annotate.WithGenicParts | Annotate given object with gene annotation |
| annotateWithFeature | Annotate object with a set of genomic features |
| annotateWithFeature-method | Annotate object with a set of genomic features |
| annotateWithFeatureFlank | Annotate an object with two sets of genomic features |
| annotateWithFeatureFlank-method | Annotate an object with two sets of genomic features |
| annotateWithGenicParts | Annotate given object with gene annotation |
| annotateWithGenicParts-method | Annotate given object with gene annotation |
| annotationByFeature | An S4 class for overlap of target features with a generic annotation |
| annotationByFeature-class | An S4 class for overlap of target features with a generic annotation |
| annotationByGenicParts | An S4 class for overlap of target features with gene annotation |
| annotationByGenicParts-class | An S4 class for overlap of target features with gene annotation |
| assocComp | Associate principal components with sample annotations |
| bedgraph | Get bedgraph from methylRaw, methylRawList and methylDiff objects |
| bedgraph-method | Get bedgraph from methylRaw, methylRawList and methylDiff objects |
| 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. |
| 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 |
| extract | extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data |
| extract-method | extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data |
| 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 |
| get.methylDiff | get differentially methylated regions/bases based on cutoffs |
| getAssembly | get assembly of the genome |
| getAssembly-method | get assembly of the genome |
| getAssociationWithTSS | Get distance to nearest TSS and gene id from annotationByGenicParts |
| getAssociationWithTSS-method | Get distance to nearest TSS and gene id from annotationByGenicParts |
| 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 | Get the percentage/count of annotation features overlapping with target features |
| getFeatsWithTargetsStats-method | Get the percentage/count of annotation features overlapping with target features |
| getFlanks | Get upstream and downstream adjacent regions to a genomic feature |
| getFlanks-method | Get upstream and downstream adjacent regions to a genomic feature |
| getMembers | Get the membership slot of annotationByFeature |
| getMembers-method | Get the membership slot of annotationByFeature |
| 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 | Get the percentage of target features overlapping with annotation from annotationByFeature |
| getTargetAnnotationStats-method | Get the percentage of target features overlapping with annotation from annotationByFeature |
| 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 |
| 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. |
| normalizeCoverage | normalize read coverage between samples |
| normalizeCoverage-method | normalize read coverage between samples |
| 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 | Plot annotation categories from annotationByGenicParts or annotationByFeature |
| plotTargetAnnotation-method | Plot annotation categories from annotationByGenicParts or annotationByFeature |
| 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 |
| read | read file(s) to methylRaw or methylRawList objects |
| read.bed | read a bed file and convert it to GRanges |
| read.bismark | Get methylation percentage from sorted Bismark alignments |
| read.feature.flank | a function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores |
| read.transcript.features | Read transcript features from a BED file |
| readBed | read a bed file and convert it to GRanges |
| readBed-method | read a bed file and convert it to GRanges |
| readFeatureFlank | a function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores |
| readFeatureFlank-method | a function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores |
| readTranscriptFeatures | Read transcript features from a BED file |
| readTranscriptFeatures-method | Read transcript features from a BED file |
| 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 |
| 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 |
| tileMethylCounts | Get methylated/unmethylated base counts for tilling windows |
| tileMethylCounts-method | Get methylated/unmethylated base counts for tilling windows |
| 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. |
| [-method | extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data |