🚧 Under Development 🚧
This package is still in development and not yet ready for general use. Proceed with caution!
The goal of MethylSurroGetR is to offer user-friendly tools and functions for generating predicted values from existing DNA methylation surrogates. It aims to enhance the accessibility and reproducibility of data analysis with methylation surrogates.
Installation
You can install the development version of MethylSurroGetR from GitHub with:
# install.packages("remotes")
remotes::install_github("jagoode27/MethylSurroGetR")Example
This is a basic example workflow:
library(MethylSurroGetR)
# Load example data
data(beta_matrix_comp)
data(wts_df)
data(ref_df)
# Create weights vector
wts_vec <- setNames(wts_df$wt_lin, rownames(wts_df))
# Create surrogate object
my_surro <- surro_set(
methyl = beta_matrix_comp,
weights = wts_vec,
intercept = "Intercept"
)
# Fill missing probes with reference values
ref_vec <- setNames(ref_df$mean, rownames(ref_df))
my_surro <- reference_fill(my_surro, reference = ref_vec)
# Calculate predictions
predictions <- surro_calc(my_surro, transform = "linear")Getting Help
See the Getting Started vignette for detailed examples and workflows.
For bug reports and feature requests, please open an issue.