Functions to conduct quality control analysis in methylation data

Documentation for package ‘scmeth’ version 1.29.0

scmeth-package	scmeth: a package to conduct quality control analysis for methylation data. Most functions can be applied to both bulk and single-cell methylation while other functions are specific to single-cell methylation data. scmeth is especially customized to use the output from the FireCloud implementation of methylation pipeline to produce comprehensive quality control report
bsConversionPlot	Bisulfite conversion rate visualization
chromosomeCoverage	CpG covergae in each chromosome
coverage	Coverage for single cells
cpgDensity	Provides Coverage by the CpG density. CpG Density is defined as the number of CpGs observed in certain base pair long region.
cpgDiscretization	Discretize the CpG methylation values to align with single cell analysis
downsample	Downsample analysis
featureCoverage	Coverage based on the genomic feature
mbiasplot	Methylation bias plot
methylationDist	Provide graphics for methylation distribution
readmetrics	Provide graphics for read information
repMask	Provides Coverage metrics in the repeat masker region
report	Generates an inclusive report on methylation analysis
scmeth	scmeth: a package to conduct quality control analysis for methylation data. Most functions can be applied to both bulk and single-cell methylation while other functions are specific to single-cell methylation data. scmeth is especially customized to use the output from the FireCloud implementation of methylation pipeline to produce comprehensive quality control report