How cruk-mi/mesa works
mesa is an R package for analysing methylation-enrichment sequencing data from MEDIP-seq or MBD-seq. The principal workflow is: a researcher supplies enriched sequencing data, constructs a qseaSet, applies tidy transformations and quality control, then performs enrichment, differential-region, dimensionality, CNV, annotation, and visualization tasks. The qseaSet is the central in-memory state layer. Relationships are conservative because no source excerpts were supplied; optional array, genome, and reference-region capabilities are shown without asserting unsupported call order.
Components 18
Input & State
- Qset Construction
R/makeQset.R - qseaSet State
R/classes.R
Transform & QC
- Tidy Qset Verbs
R/dplyrVerbs.R - Qset Combination
R/combineQsets.R - Sample QC
R/sampleQC.R - Methylation Enrichment
R/calculateEnrichment.R
Statistical Analysis
- DMR Analysis
R/analyseDMRs.R - DMR Generation
R/makeDMRs.R - PCA Analysis
R/PCA.R - CNV Analysis
R/qseaCNV.R - Array Integration
R/alterQset.R
Annotation & Visualization
- Window Annotation
R/utilityFunctions.R - Plots & Heatmaps
R/plotting.R - Result Tables
R/qseaExtra.R
Reference Data
- Genome Mapping
R/map_hg38.R - Reference Regions
R/ENCODEbadRegions.R
Other components
- Researcher
- Enriched Sequencing Data
Connections 17
- Researcher → Enriched Sequencing Data: supplies data
- Enriched Sequencing Data → Qset Construction: loads data
- Qset Construction → qseaSet State: creates state
- qseaSet State → Tidy Qset Verbs: passes qset
- qseaSet State → Qset Combination: combines qsets
- qseaSet State → Sample QC: supports QC
- qseaSet State → Methylation Enrichment: calculates enrichment
- qseaSet State → DMR Analysis: analyses regions
- qseaSet State → DMR Generation: makes DMRs
- qseaSet State → PCA Analysis: runs PCA
- qseaSet State → CNV Analysis: analyses CNV
- qseaSet State → Array Integration: mixes array data
- qseaSet State → Window Annotation: annotates windows
- qseaSet State → Plots & Heatmaps: plots qset
- qseaSet State → Result Tables: extracts results
- Genome Mapping → Window Annotation: maps coordinates
- Reference Regions → Window Annotation: provides regions