Struct lightmotif::pwm::CountMatrix

pub struct CountMatrix<A: Alphabet> { /* private fields */ }

A matrix storing symbol occurrences at each position.

Implementations

impl<A: Alphabet> CountMatrix<A>

pub fn new(data: DenseMatrix<u32, A::K>) -> Result<Self, InvalidData>

Create a new count matrix from the given data.

The matrix must contain count data, for sequences of the same length, i.e. rows should all sum to the same value.

pub fn from_sequences<'seq, I>(sequences: I) -> Result<Self, InvalidData>

where I: IntoIterator, <I as IntoIterator>::Item: AsRef<EncodedSequence<A>>,

Create a new count matrix from the given sequences.

Errors

This function returns Err(InvalidData) when the sequences do not all have the same length:

let result = CountMatrix::<Dna>::from_sequences([
    EncodedSequence::new(vec![T, T, A, T]),
    EncodedSequence::new(vec![T, C, A]),
]);
assert!(result.is_err());

pub fn to_freq<P>(&self, pseudo: P) -> FrequencyMatrix<A>

where P: Into<Pseudocounts<A>>,

Build a probability matrix from this count matrix using pseudo-counts.

pub fn entropy(&self) -> Vec<f32>

Compute the entropy of each column of the matrix.

The entropy of a column, sometimes refered to as “uncertainty”, is computed by treating each motif position as a random variable taking values in alphabet A.

pub fn information_content(&self) -> f32

Compute the information content of the matrix.

impl<A: ComplementableAlphabet> CountMatrix<A>

pub fn reverse_complement(&self) -> Self

Get the reverse-complement of this count matrix.

impl<A: Alphabet> CountMatrix<A>

pub fn matrix(&self) -> &DenseMatrix<u32, A::K>

The raw data storage for the matrix.

Trait Implementations

impl<A: Alphabet> AsRef<CountMatrix<A>> for CountMatrix<A>

fn as_ref(&self) -> &Self

Converts this type into a shared reference of the (usually inferred) input type.

impl<A: Alphabet> AsRef<DenseMatrix<u32, <A as Alphabet>::K>> for CountMatrix<A>

fn as_ref(&self) -> &DenseMatrix<u32, A::K>

Converts this type into a shared reference of the (usually inferred) input type.

impl<A: Clone + Alphabet> Clone for CountMatrix<A>

where A::K: Clone,

fn clone(&self) -> CountMatrix<A>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<A: Debug + Alphabet> Debug for CountMatrix<A>

where A::K: Debug,

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

Formats the value using the given formatter.

impl<A: Alphabet> Index<usize> for CountMatrix<A>

type Output = <DenseMatrix<u32, <A as Alphabet>::K> as Index<usize>>::Output

The returned type after indexing.

fn index(&self, index: usize) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<A: PartialEq + Alphabet> PartialEq for CountMatrix<A>

where A::K: PartialEq,

fn eq(&self, other: &CountMatrix<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<A: Eq + Alphabet> Eq for CountMatrix<A>

where A::K: Eq,

impl<A: Alphabet> StructuralPartialEq for CountMatrix<A>