Principal Component BiSulfite

Documentation for package ‘PCBS’ version 0.1.1

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()