Man pages for PCBS
Principal Component BiSulfite
| addRanks | Add ranks to eigenvector scores. |
| CheckOvercompression | Check if DMR calling seed number is ovcompressed. |
| checkRank | Check rank cut-off values manually. |
| chromDict | Convert a rank object into a chromDict. |
| chromDictMeth | Create a chromDict of percent methylation difference at all... |
| DefineBestPC | Identify your best principle component. |
| eigen | Simulated WGBS data for PCBS vignettes |
| get_all_DMRs | Nested DMR calling function within Get_Novel_DMRs() |
| Get_Novel_DMRs | Call DMRs from WGBS data. |
| getPCRanks | Get CpG eigenvector scores from a principle component. |
| getRegionScores | Calculated methylation significance in a set of regions. |
| lin | Find y value of linear regression given x. |
| lmIntx | PC-Intersect nested function. |
| MethyDiff_Set | Add a mean methylation column to a data.frame of regions. |
| MethylDiff | Get the mean methylation difference across a specified... |
| methylDiff_metagene | Make a metagene from mean percent methylation differences. |
| multiple_metagenes | Plot multiple metagene data objects on a single plot. |
| Ol_Reliable | PCBS ggplot theme. |
| oneSeed | Nested DMR calling function within within get_all_DMRs(),... |
| plot_metagene | Generate a metagene plot from raw metagene data. |
| rankDist | Identify the best rank cut-off for significant CpGs. |
| score_metagene | Make a metagene from PC Scores. |
| se | Standard error of a vector. |
| tilt | Component of PCBS ggplot theme. |
| trimDMR | Nested DMR calling function within within Get_Novel_DMRs() |
