Project: s41467-025-59117-2 | Function: myArchR_peak2geneLinkage (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Custom implementation for linking chromatin accessibility peaks to genes. Extends ArchR functionality for peak-to-gene regulatory linkage analysis.

**KEY TERMS:** {
  "peak2geneLinkage": "regulatory element linking",
  "ArchR": "chromatin accessibility analysis",
  "linkage": "regulatory connections"
}

**CONTEXT CODE:** # Minimal masked version of ArchR_peak2geneLinkage.R for testing
# Contains masked functions for proper test failure

# Source mock functions if needed
if (!exists("GetAssayData")) {
  # Try different paths depending on where the script is run from
  mock_paths <- c(
    "mock_functions.R",           # Same directory
    "../../mock_functions.R",     # From tests/testthat
    "../mock_functions.R"         # From tests
  )

  for (path in mock_paths) {
    if (file.exists(path)) {
      source(path)
      break
    }
  }
}

myArchR_peak2geneLinkage <- function(seu, peak.assay='shared_ATAC', peak.slot='counts', rna.assay='RNA', rna.slot='data',
                                     corCutOff = 0.45, FDRCutOff = 1e-04) {
  stop("Function implementation has been masked")
}

lm_eqn2 <- function(df) {
  stop("Function implementation has been masked")
}

Complete the function implementation replacing "stop("Not implemented")".