Apply cv.glmnet() for a list of module IDs

Usage

find_all_module_neighbors(df, test_module, seed = NULL, ...)

Arguments

df: Dataframe. A normalized dataframe
test_module: List of string. The module IDs
seed: Numeric. The seed number, ensuring reproducibility
...: Additional arguments passed on to find_module_neighbors()

Value

Dataframe. Returns the module ID, its detected neighbor and the corresponding coefficient

Examples

data(data)
data(metadata)
# Simple example
x <- norm_data(data$CRC_JPN, 0.30, annotation_level = "species")[[1]]
neighbors_JPN <- find_all_module_neighbors(
  df = x,
  test_module = c("msp_0030", "msp_0345"),
  seed = 20242025
)
# Example with covariate
# x <- norm_data(data$CRC_CHN, 0.30, annotation_level = "species")[[1]]
# neighbors_CHN <- find_all_module_neighbors(
#   df = x,
#   test_module = c("msp_0030", "msp_0345"),
#   seed = 20242025,
#   covar = ~study_accession,
#   meta_df = metadata$CRC_CHN,
#   sample_col = "secondary_sample_accession"
# )