methylQC

Quality control for methylome data

Install

Install from github

# install.packages("devtools")
devtools::install_github("timoast/methylqc")

loadData: Loads a BSseeker2 CGmap file into memory. This just calls data.table::fread and gives each column the correct names.
cytosines: Count the number of cytosines in each sequence context, for each chromosome, using a given fasta file.
plotBrowser: Generate a genome browser view of sequencing coverage for a given genomic region.
coverageSurvival: Calculate the diminishing percentage of all cytosines with increasing levels of sequencing depth.
plotCoverage: Plot the diminishing percentage of all cytosines with increasing levels of sequencing depth.
methylomeStats: Generate some summary statistics for the distribution of sequencing depth. This returns a dataframe with the quantiles, mean, and kurtosis (how "spiky" the coverage is).
nonConversion: Calculate the bisulfite non-conversion rates for each sequence context.
strandBias: Calculate bias in sequencing depth towards either strand for each C position.

methylome: A small test dataset including sequencing data for the lambda genome and the first ~1 million cytosines of Arabidopsis chromosome 1.
arabidopsis: Cytosine information for the Arabidopsis genome.

This package is also implemented in an interactive app built using shiny, available here: