Sliding Window Entropy Scan — sliding_window

Perform a sliding window scan across a DNA sequence to calculate entropy and KL divergence metrics at each position. This is the main function for de novo ORF discovery.

Usage

sliding_window_scan(
  sequence,
  window_size = 300,
  step_size = 30,
  reference_profile = NULL,
  min_codons = 10
)

Arguments

sequence: Character string or DNAString object representing DNA sequence
window_size: Integer size of sliding window in base pairs (default: 300)
step_size: Integer step size for sliding window (default: 30)
reference_profile: Optional reference codon frequency profile. If NULL, only Shannon entropy is calculated.
min_codons: Minimum number of complete codons required for analysis (default: 10)

Value

A data frame with window coordinates and entropy metrics

Examples

sequence <- paste(rep("ATGATGATGTTATTATTACGCCGCCGCC", 20), collapse = "")
result <- sliding_window_scan(sequence, window_size = 150, step_size = 30)