Functions to conduct quality control analysis in methylation data


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Documentation for package ‘scmeth’ version 1.28.0

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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