Generate a QC summary report for a whole data set

[bdecato]

Description

As a bioinformatician, I would like to generate an automated summary of methylation levels in various genomic regions of interest, in order better understand the biological system of interest.

Estimate

5

Priority

SHOULD

Notes

• Input will be the results of Calculate average DNA methylation across regions of interest #29 run across a whole data set
• Output should be one R Markdown webpage consisting of violin/boxplots showing the regional distribution of methylation levels in gene promoters, gene bodies, retrotransposons, and intergenic regions, etc.
• Also useful would be a boxplot/beeswarm plot of number of CpGs covered per library

For later:

• Another useful plot would be the counts of coverage at each CpG (just a barplot, maybe pooled across all cells, probably on a log scale)