Apply cv.glmnet() for a given mmodule ID

Usage

find_module_neighbors(
  df,
  module,
  seed = NULL,
  covar = NULL,
  meta_df = NULL,
  sample_col = NULL
)

Arguments

df: Dataframe. A normalized dataframe
module: String. The module ID name
seed: Numeric. The seed number, ensuring reproducibility
covar: String or formula. Formula or the name of the column of the covariate in the metadata table. Note that "study_accession" is equivalent to ~study_accession
meta_df: Dataframe. The dataframe giving metadata information
sample_col: String. The name of the column in metadata indicating the sample names, it should be consistent with the colnames of 'df'

Value

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

Examples

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