methyl_surro Objects

The methyl_surro class is the core data structure in MethylSurroGetR. It stores methylation data aligned with surrogate weights, ready for calculation of surrogate predictions. Objects of this class are created by surro_set and modified by reference_fill and impute_obs.

Object Structure

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

methyl: A numeric matrix with CpG sites as rows (with CpG IDs as row names) and samples as columns (with sample IDs as column names). Values represent methylation levels, typically as beta values (0-1 scale) or M-values (log-ratio scale).
weights: A named numeric vector where names are CpG site IDs and values are the regression coefficients for each probe in the surrogate model. The intercept term is stored separately (see below).
intercept: A single numeric value representing the intercept term of the surrogate model, or NULL if no intercept is included.

Creating methyl_surro Objects

Objects are created using surro_set:


# Load data
data(beta_matrix_comp)
data(wts_df)

# Create weights vector
wts_vec <- setNames(wts_df$wt_lin, rownames(wts_df))

# Create methyl_surro object
my_surro <- surro_set(
  methyl = beta_matrix_comp,
  weights = wts_vec,
  intercept = "Intercept"
)

Accessing Components

Components can be accessed using standard list notation:


# Access methylation matrix
methyl_data <- my_surro$methyl

# Access weights
weight_values <- my_surro$weights

# Access intercept
intercept_value <- my_surro$intercept

Modifying methyl_surro Objects

methyl_surro objects can be modified by:

reference_fill: Fills missing probes and/or observations with reference values
impute_obs: Imputes missing observations using mean or median values

These functions return modified methyl_surro objects, optionally with additional statistics components (see below).

Optional Statistics Components

When reference_fill or impute_obs are called with return_stats = TRUE, the returned object may contain additional components:

reference_fill_stats: An object of class reference_fill_stats containing detailed information about the reference filling operation (see reference_fill_stats).
imputation_stats: An object of class imputation_stats containing detailed information about the imputation operation (see imputation_stats).

Using methyl_surro Objects

Once properly prepared, methyl_surro objects are used with surro_calc to calculate surrogate predictions:


# Calculate predictions
predictions <- surro_calc(my_surro, transform = "linear")