reference_fill_stats Objects

The reference_fill_stats class stores detailed information about a reference filling operation performed by reference_fill. These objects provide comprehensive statistics about what was filled and how the missing data was addressed.

Object Structure

A reference_fill_stats object is a list with class "reference_fill_stats" containing:

type: Character string indicating the fill type used: "probes" (only completely missing probes), "obs" (only missing observations), or "all" (both).
timestamp: POSIXct timestamp of when filling was performed.
n_total_probes: Total number of probes in the methylation matrix.
n_total_samples: Total number of samples in the methylation matrix.
n_completely_missing_probes_before: Number of completely missing probes before filling.
n_completely_missing_probes_after: Number of completely missing probes after filling.
n_probes_filled: Number of completely missing probes that were filled.
n_obs_filled: Number of individual missing observations that were filled (in partially missing probes).
n_total_values_filled: Total number of values filled (sum of probes filled × samples + individual observations filled).
n_missing_before: Total missing values before filling.
n_missing_after: Total missing values after filling.
fill_rate: Proportion of originally missing values that were filled (0 to 1).
probes_filled: Character vector of CpG probe IDs for completely missing probes that were filled.
obs_filled: Character vector of CpG probe IDs for probes that had individual observations filled.
values_filled_per_probe: Named numeric vector showing the number of values filled for each probe (only present when return_stats = TRUE).
probes_not_in_reference: Character vector of CpG probe IDs that were missing but not present in the reference values (only present when applicable).

Creating reference_fill_stats Objects

Objects are created automatically when calling reference_fill with return_stats = TRUE:


# Perform reference filling with statistics
result <- reference_fill(
  my_surro,
  reference = ref_values,
  type = "probes",
  return_stats = TRUE
)

# Access the statistics
stats <- result$reference_fill_stats

Accessing Information

Components can be accessed using standard list notation:


# View filling summary
stats$n_total_values_filled
stats$fill_rate

# View which probes were filled
stats$probes_filled

# View detailed filling counts
stats$values_filled_per_probe

Print Method

The package provides a print method that displays a formatted summary:


print(stats)

This shows an organized view of the reference filling operation and its results.

Object Structure

Creating reference_fill_stats Objects

Accessing Information

Print Method

See also