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Synthetic example methylation dataset for the comma package

Source: R/comma_example_data.R
comma_example_data.Rd

A commaData object built from simulated Oxford Nanopore methylation data. This dataset is used in package examples, vignettes, and tests. It does not represent real biological data.

Format

A commaData object with:

Sites

300 methylation sites (200 × 6mA, 100 × 5mC) on a simulated 100 kb chromosome ("chr_sim").

Samples

3 samples: ctrl_1 and ctrl_2 (condition "control") and treat_1 (condition "treatment").

Assays
methylation

Beta values (proportion methylated reads, 0–1). NA where coverage < 5.

coverage

Integer read depth (10–50 per site).

rowData

Per-site metadata including chrom, position, strand, mod_type, and is_diff (ground-truth differential methylation status for testing purposes).

colData

Per-sample metadata: sample_name, condition, replicate, caller.

genomeInfo

Named integer vector: c(chr_sim = 100000L).

annotation

5 simulated genomic features (genes, rRNA, tRNA).

motifSites

Empty GRanges (no motif search was run).

Source

Simulated data generated by data-raw/create_example_data.R

Value

A commaData object (see Details and Format sections above for structure).

Details

The dataset simulates an experiment where ~30 of the 200 6mA sites are differentially methylated between control and treatment conditions. Control samples have high methylation at these sites (~0.9 beta), while the treatment sample has low methylation (~0.25 beta). This ground truth is stored in rowData(comma_example_data)$is_diff for use in testing diffMethyl() (implemented in Phase 4).

5mC sites are not differentially methylated and serve to test multi- modification-type functionality.

The dataset was generated by data-raw/create_example_data.R using set.seed(1312).

Examples

data(comma_example_data)
comma_example_data
#> class: commaData
#> sites: 300 | samples: 6 
#> mod types: 5mC, 6mA 
#> conditions: control, treatment 
#> genome: 1 chromosome (100,000 bp total) 
#> annotation: 5 features 
#> motif sites: none 
modTypes(comma_example_data)
#> [1] "5mC" "6mA"
sampleInfo(comma_example_data)
#>         sample_name condition replicate caller
#> ctrl_1       ctrl_1   control         1 modkit
#> ctrl_2       ctrl_2   control         2 modkit
#> ctrl_3       ctrl_3   control         3 modkit
#> treat_1     treat_1 treatment         1 modkit
#> treat_2     treat_2 treatment         2 modkit
#> treat_3     treat_3 treatment         3 modkit
dim(methylation(comma_example_data))
#> [1] 300   6