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()
