methylkit-database-mode-configuration

methylkit-database-mode-configuration

Summary

Configure methylKit to store methylation data in tabix-indexed bgzipped files on disk rather than in memory, enabling scalable analysis of large bisulfite sequencing datasets. This skill uses the methRead() function with dbtype='tabix' parameter to create memory-efficient methylRawListDB objects backed by external indexed files.

When to use

When analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when you need to process multiple large samples sequentially without reloading data. Specifically, use this skill when you have CpG methylation call files and want to avoid the memory overhead of storing all methylation data in RAM while preserving fast random access to per-base methylation information.

When NOT to use

• Input data is already loaded as an in-memory methylRawList or methylBase object — direct conversion or in-memory analysis is more efficient.
• Dataset is small enough to fit comfortably in RAM and analysis speed is critical over memory efficiency.
• Bismark or methylation call files are not in a format recognized by methRead() or lack required metadata headers for tabix indexing.

Inputs

• CpG methylation call files (typically in Bismark or similar format)
• dbtype parameter specification ('tabix')
• bgzipped tabix-indexed methylation data files on disk

Outputs

• methylRawListDB object with disk-backed storage
• methylRaw objects with populated dbpath slots referencing external tabix files
• Validated tabix file index structures with methylKit metadata headers

How to apply

Load CpG methylation call files using the methRead() function with the dbtype='tabix' parameter to create a methylRawListDB object where each methylRaw object maintains a dbpath slot referencing bgzipped tabix-indexed files on disk. The tabix files must contain methylKit metadata headers (version ≥ 1.13.1) and be properly indexed. Verify that the resulting object's structure matches methylKit database-mode standards by inspecting the dbpath slot to confirm valid file paths and examining tabix file headers for metadata integrity. This configuration enables data retrieval from external files rather than memory storage, making it suitable for large-scale methylation studies where coverage statistics and methylation percentages are queried selectively rather than loaded entirely into RAM.