Struct Pedigree

pub struct Pedigree(/* private fields */);

A pedigree describes the divergence bewteen any two samples in a population. It’s a matrix with four columns, containing the following information:

t0: The generation of the last common ancestor between two samples (Can be one of the samples if direct heritage).

t1: The generation of the first sample.

t2: The generation of the second sample.

d: The divergence between the two samples.

The length of the pedigree is the number of possible pairs of samples, for which methlyation data is available => n * (n - 1) / 2

Implementations

impl Pedigree

pub fn from_file(filename: &str) -> Self

Read a pedigree from a file.

The file must be a tab-separated file with four columns:

t0: The generation of the last common ancestor between two samples (Can be one of the samples if direct heritage).

t1: The generation of the first sample.

t2: The generation of the second sample.

d: The divergence between the two samples.

The first line of the file is ignored. I chose not to return a result, as this function is meant to statically read a file and therefore it is preferable to panic if the file is not found or parsing errors occur.

pub fn to_file<P>(&self, path: P) -> Result<()>

where P: AsRef<Path> + Debug,

pub fn build<P>( nodelist: P, edgelist: P, posterior_max_filter: f64, ) -> Return<(Self, f64)>

where P: AsRef<Path>,

Trait Implementations

impl Clone for Pedigree

fn clone(&self) -> Pedigree

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Pedigree

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Deref for Pedigree

type Target = ArrayBase<OwnedRepr<f64>, Dim<[usize; 2]>>

The resulting type after dereferencing.

fn deref(&self) -> &Self::Target

Dereferences the value.

impl DerefMut for Pedigree

fn deref_mut(&mut self) -> &mut Self::Target

Mutably dereferences the value.