Create Default Additional Features — create_default_additional

This function generates additional features for a given set of peaks. The features include sequence features and regional ATAC signal using a punctured window.

Usage

create_default_additional_features(
  peaks,
  tracks,
  window_size = 20000,
  normalize = TRUE,
  norm_quant = 0.05,
  spatial_ratio_ext = 1000
)

Arguments

peaks: Intervals set of peaks
tracks: Tracks containing ATAC signal
window_size: An integer specifying the size of the window for computing regional ATAC signal. Default is 20,000 bp.
normalize: A logical value indicating whether to normalize the features to the range 0-10.
norm_quant: The quantile to use for normalization. Values below this quantile and above 1-quantile are truncated, and the rest are linearly scaled to 0-10.

Value

A data frame with additional features: sequence features and regional ATAC signal. The features are normalized to the range 0-10.