R: Functions to conduct quality control analysis in methylation data

# Functions to conduct quality control analysis in methylation data

## Documentation for package ‘scmeth’ version 1.33.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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