Expand description
Tools for working with site frequency spectra.
This serves as the core library implementation for the sfs CLI, but can also be used as a
free-standing library for working with frequency spectra.
§Overview
The core struct is a Spectrum, which is backed by an N-dimensional Array.
A spectrum may either be a frequency spectrum (Sfs), in which case we say that it is
normalized, or it may be a count spectrum (Scs).
§Example
As a very brief introduction to the API, let’s create a count spectrum, and then normalize it to obtain a per-base estimate of θ using Watterson’s estimator.
use sfs_core::Scs;
// Create a 1-dimensional SCS from some data
let scs = Scs::from_vec([25., 8., 4., 2., 1., 0.]);
// Normalize the spectrum to frequencies
let sfs = scs.into_normalized();
// Calculate θ
let theta = sfs.theta_watterson().expect("θ only defined in 1D");
assert!((theta - 0.18).abs() < 1e-16);Re-exports§
pub use input::Input;pub use spectrum::Scs;pub use spectrum::Sfs;pub use spectrum::Spectrum;pub use array::Array;