Function reference • PCBS

All functions
`CheckOvercompression()`	Check if DMR calling seed number is ovcompressed.
`DefineBestPC()`	Identify your best principle component.
`Get_Novel_DMRs()`	Call DMRs from WGBS data.
`MethyDiff_Set()`	Add a mean methylation column to a data.frame of regions.
`MethylDiff()`	Get the mean methylation difference across a specified region.
`Ol_Reliable()`	PCBS ggplot theme.
`addRanks()`	Add ranks to eigenvector scores.
`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.
`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()
`lin()`	Find y value of linear regression given x.
`lmIntx()`	PC-Intersect nested function.
`methylDiff_metagene()`	Make a metagene from mean percent methylation differences.
`multiple_metagenes()`	Plot multiple metagene data objects on a single plot.
`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()

Reference