# Principal Component BiSulfite

## Documentation for package ‘PCBS’ version 0.1.1

- DESCRIPTION file

## Help Pages

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 sites.
DefineBestPC | Identify your best principle component.
eigen | Simulated WGBS data for PCBS vignettes
getPCRanks | Get CpG eigenvector scores from a principle component.
getRegionScores | Calculated methylation significance in a set of regions.
get_all_DMRs | Nested DMR calling function within Get_Novel_DMRs()
Get_Novel_DMRs | Call DMRs from WGBS data.
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 region.
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(), Get_Novel_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()