mesa is an R package for Methylation Enrichment Sequencing Analysis, to investigate sequencing data that has been enriched for regions of CG methylation. This includes both MEDIP-Seq (Methylated DNA immunoprecipitation sequencing) or MBD-seq (methyl-CpG binding domain protein enriched sequencing).
This package builds off the qsea package, using the qseaSet object type defined in that package as the object that holds the data. One of the most useful features of the package is in defining tidyverse verbs to act on a qseaSet, such as filter, mutate and select, but there also includes a range of functionality for other tasks, such as plotting and quality control.
This package has been used in a Nature Cancer paper, [cfDNA methylome profiling for detection and subtyping of small cell lung cancers] [https://www.nature.com/articles/s43018-022-00415-9), as well as an in CUPiD: A cfDNA methylation-based tissue-of-origin classifier for Cancers of Unknown Primary.
Development was undertaken internally between September 2022 and March 2024; these commits are now incorporated into this repository. This has involved an extensive rewriting of the package functions, with many function names changing, see the NEWS.md file for all the details.
The package is under active development with plans to submit to BioConductor, and a full vignette is under construction. If you are interested in using the package, we're happy to hear from you.
Currently, the easiest way to install the package is with devtools:
install.packages("devtools")
devtools::install_github("cruk-mi/mesa")