Man pages for fortunatobianconi/methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results
| adjust.methylC | Adjust measured 5mC levels using 5hmC levels |
| annotate.WithFeature.Flank-methods | Annotate an object with two sets of genomic features |
| annotate.WithFeature-methods | Annotate object with a set of genomic features |
| annotate.WithGenicParts-methods | Annotate given object with gene annotation |
| annotationByFeature-class | An S4 class for overlap of target features with a generic... |
| annotationByGenicParts-class | An S4 class for overlap of target features with gene... |
| annotationByGenicParts-methods | Get distance to nearest TSS and gene id from... |
| assocComp-methods | Associate principal components with sample annotations |
| bedgraph-methods | Get bedgraph from methylRaw, methylRawList and methylDiff... |
| calculateDiffMeth-methods | Calculate differential methylation statistics |
| clusterSamples-methods | Hierarchical Clustering using methylation data |
| diffMethPerChr-methods | Get and plot the number of hyper/hypo methylated... |
| extract-methods | extract parts of methylRaw,methylBase and methylDiff data |
| filterByCoverage-methods | Filter methylRaw and methylRawList object based on read... |
| getAssembly-methods | get assembly of the genome |
| getContext-methods | get the context of methylation |
| getCorrelation-methods | get correlation between samples in methylBase object |
| getCoverageStats-methods | get coverage stats from methylRaw object |
| getData-methods | get the data slot from the methylKit objects |
| getFeatsWithTargetsStats-methods | Get the percentage/count of annotation features overlapping... |
| getFlanks-methods | Get upstream and downstream adjacent regions to a genomic... |
| getMembers-methods | Get the membership slot of annotationByFeature |
| getMethylationStats-methods | get Methylation stats from methylRaw object |
| get.methylDiff-methods | get differentially methylated regions/bases based on cutoffs |
| getTargetAnnotationStats-methods | Get the percentage of target features overlapping with... |
| methylBase-class | An S4 class for methylation events sampled in multiple... |
| methylBase.obj | Example methylBase object. |
| methylDiff-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... |
| methylRawList-class | An S4 class for holding a list of methylRaw 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 object |
| plotTargetAnnotation-methods | Plot annotation categories from annotationByGenicParts or... |
| pool-methods | Pool replicates within groups to a single sample per group |
| read.bed-methods | read a bed file and convert it to GRanges |
| read.bismark-methods | Read from sorted Bismark SAM files |
| read.feature.flank-methods | a function to read-in genomic features and their upstream and... |
| read-methods | read file(s) to a methylrawList or methylraw object |
| read.transcript.features-methods | Read transcript features from a BED file |
| reconstruct-methods | Reconstruct methylBase object based on a new methylation... |
| 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... |
| 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 |
