methyl_miss Objects

The methyl_miss class stores comprehensive information about missing data patterns in a methyl_surro object. Objects of this class are created by the methyl_miss function and provide detailed summaries of both partial and complete missingness.

Object Structure

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

missing_obs: A named numeric vector showing the proportion of missing observations (0 to 1) for each probe that has partial missingness (i.e., missing in some but not all samples). Names are CpG probe IDs.
missing_probes: A character vector of CpG probe IDs that are completely missing (i.e., missing in all samples).
summary: A list containing overall summary statistics (see details below).

Summary Statistics

The summary component contains:

total_probes: Total number of CpG probes in the methylation matrix.
total_samples: Total number of samples in the methylation matrix.
n_complete_probes: Number of probes with no missing values.
n_missing_obs: Number of probes with partial missing data (some but not all samples missing).
n_missing_probes: Number of completely missing probes (all samples missing).
overall_missing_rate: Proportion of all matrix values that are missing (0 to 1).
missing_obs_rate: Proportion of probes with partial missing data (0 to 1).
missing_probes_rate: Proportion of probes that are completely missing (0 to 1).
complete_probes_rate: Proportion of probes with no missing values (0 to 1).

Creating methyl_miss Objects

Objects are created using methyl_miss:


# Create methyl_surro object
my_surro <- surro_set(beta_matrix_miss, weights_vec, "Intercept")

# Assess missing data
miss_info <- methyl_miss(my_surro)

Accessing Information

Components can be accessed using standard list notation:


# View probes with partial missingness
miss_info$missing_obs

# View completely missing probes
miss_info$missing_probes

# Access summary statistics
miss_info$summary$overall_missing_rate
miss_info$summary$n_missing_probes

Print Method

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


print(miss_info)

This shows an organized view of missing data patterns and summary statistics.

Object Structure

Summary Statistics

Creating methyl_miss Objects

Accessing Information

Print Method

See also