Package index • MethylSurroGetR

Setting Up Surrogates

Initialize your surrogate object

surro_set(): Create a methyl_surro Object

Missing Data Handling

Assess and address missing methylation data

methyl_miss(): Summarize Missing Data in methyl_surro Object
reference_fill(): Fill Missing Probes in methyl_surro Object Using Reference Data
impute_obs(): Impute Missing Observations in methyl_surro Object

Calculate Predictions

Compute surrogate predictions from methylation data

surro_calc(): Calculate Predicted Values from methyl_surro Object

Data Conversion

Convert between beta values and M-values

convert_beta_to_m(): Convert Beta Values to M-Values
convert_m_to_beta(): Convert M-Values to Beta Values

Object Classes

Documentation for S3 object classes used in the package

methyl_surro: methyl_surro Objects
methyl_miss-class: methyl_miss Objects
imputation_stats: imputation_stats Objects
reference_fill_stats: reference_fill_stats Objects

Print Methods

S3 print methods for package objects

print(<imputation_stats>): Print Method for imputation_stats Objects
print(<methyl_miss>): Print Method for methyl_miss Objects
print(<reference_fill_stats>): Print Method for reference_fill_stats Objects

Example Data

Sample datasets included with the package

beta_matrix_comp: Complete Beta Matrix without Missing Values
beta_matrix_miss: Beta Matrix with Missing Values
mval_matrix_comp: Complete M-Values Matrix
mval_matrix_miss: M-Values Matrix with Missing Values
wts_df: Regression Weights Data Frame
ref_df: Reference Values Data Frame