Create Sequence Features — create_sequence

This function generates sequence features from given intervals. It calculates dinucleotide frequencies and GC content, normalizes these features, and returns them as a matrix.

Usage

create_sequence_features(
  intervals,
  size = NULL,
  normalize = TRUE,
  norm_quant = 0.05,
  norm_intervals = NULL
)

Arguments

intervals: A data frame containing interval information with columns start and end.
size: The size of the sequences to extract. If NULL, the size is calculated from the first interval.
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.
norm_intervals: Optional. A data frame of intervals to use for computing normalization quantiles. If NULL, quantiles are computed from the input intervals.

Value

A matrix of normalized sequence features including GC content and dinucleotide frequencies.