Summarize per-sample methylation and coverage distributions

Computes per-sample summary statistics for methylation beta values and sequencing coverage in a commaData object. Returns a tidy data.frame suitable for direct use with ggplot2 or for tabular reporting.

Usage

methylomeSummary(object, mod_type = NULL)

Arguments

object

A commaData object.

mod_type

Character string or NULL. If provided, only sites of the specified modification type (e.g., "6mA") are included in the summary. If NULL (default), all modification types are summarized together.

Value

A data.frame with one row per sample, containing:

sample_name

Sample identifier.

condition

Experimental condition, from sampleInfo(object)$condition.

mod_type

The modification type summarized ("all" if mod_type = NULL).

n_sites

Total number of sites considered.

n_covered

Number of sites with non-NA methylation in this sample (i.e., sites above the coverage threshold).

mean_beta

Mean beta value across covered sites.

median_beta

Median beta value across covered sites.

sd_beta

Standard deviation of beta values across covered sites.

frac_methylated

Fraction of covered sites with \(\beta > 0.5\) (broadly methylated).

mean_coverage

Mean sequencing depth across all sites (including sites below the min_coverage threshold, which have coverage stored as 0 or their raw depth).

median_coverage

Median sequencing depth.

See also

methylation, coverage, sampleInfo

Examples

data(comma_example_data)
ms <- methylomeSummary(comma_example_data)
ms
#>   sample_name condition mod_type n_sites n_covered mean_beta median_beta
#> 1      ctrl_1   control      all     300       300 0.8678843   0.8881436
#> 2      ctrl_2   control      all     300       300 0.8728354   0.8951648
#> 3      ctrl_3   control      all     300       300 0.8781476   0.8966108
#> 4     treat_1 treatment      all     300       300 0.8135452   0.8829561
#> 5     treat_2 treatment      all     300       300 0.8136529   0.8867238
#> 6     treat_3 treatment      all     300       300 0.8004998   0.8694701
#>      sd_beta frac_methylated mean_coverage median_coverage
#> 1 0.10150073       0.9900000      76.23333            75.5
#> 2 0.09697667       0.9966667      86.88667            93.5
#> 3 0.08514535       1.0000000      81.54000            82.5
#> 4 0.19181379       0.9166667      82.13667            84.0
#> 5 0.19951744       0.9000000      78.47333            80.0
#> 6 0.21427601       0.9066667      79.93000            77.0

# Summarize only 6mA sites
ms_6mA <- methylomeSummary(comma_example_data, mod_type = "6mA")
ms_6mA[, c("sample_name", "condition", "mean_beta", "n_covered")]
#>   sample_name condition mean_beta n_covered
#> 1      ctrl_1   control 0.8986871       200
#> 2      ctrl_2   control 0.9002143       200
#> 3      ctrl_3   control 0.9090365       200
#> 4     treat_1 treatment 0.8189668       200
#> 5     treat_2 treatment 0.8187088       200
#> 6     treat_3 treatment 0.8001237       200