Struct ScoringMatrix

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

A matrix storing log-odds ratio of symbol occurrences at each position.

Implementations

impl<A: ComplementableAlphabet> ScoringMatrix<A>

pub fn reverse_complement(&self) -> Self

Get the reverse-complement of this scoring matrix.

impl<A: Alphabet> ScoringMatrix<A>

pub fn new(background: Background<A>, data: DenseMatrix<f32, A::K>) -> Self

Create a new scoring matrix from the given log-odds matrix.

pub fn background(&self) -> &Background<A>

The background frequencies of the position weight matrix.

pub fn min_score(&self) -> f32

The lowest score that can be obtained with this scoring matrix.

pub fn max_score(&self) -> f32

The highest score that can be obtained with this scoring matrix.

pub fn information_content(&self) -> f32

Compute the information content of the matrix.

pub fn score<S, C>(&self, seq: S) -> StripedScores<f32, C>

where C: StrictlyPositive + ArrayLength, S: AsRef<StripedSequence<A, C>>, Pipeline<A, Dispatch>: Score<f32, A, C>,

Compute the PSSM scores for every position of the given sequence.

Note

Uses platform-accelerated implementation when available.

pub fn score_position<S, C>(&self, seq: S, pos: usize) -> f32

where C: StrictlyPositive + ArrayLength, S: AsRef<StripedSequence<A, C>>,

Compute the score for a single sequence position.

pub fn to_discrete(&self) -> DiscreteMatrix<A>

Get a discrete matrix from this position-specific scoring matrix.

pub fn to_score_distribution(&self) -> ScoreDistribution<A>

Get the score distribution for this position-specific scoring matrix.

See crate::pwm::dist module for more information.

Note

Generating a ScoreDistribution takes time, so this method should be called only once per ScoringMatrix and the result cached for optimal performance.

impl<A: Alphabet> ScoringMatrix<A>

pub fn matrix(&self) -> &DenseMatrix<f32, A::K>

The raw data storage for the matrix.

pub fn len(&self) -> usize

Get the length of the motif encoded in this matrix.

pub fn is_empty(&self) -> bool

Check whether the matrix is empty.

Trait Implementations

impl<A: Alphabet> AsRef<DenseMatrix<f32, <A as Alphabet>::K>> for ScoringMatrix<A>

fn as_ref(&self) -> &DenseMatrix<f32, A::K>

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

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

fn as_ref(&self) -> &Self

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

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

where A::K: Clone,

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

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<A: Alphabet> Correlation for ScoringMatrix<A>

fn num_rows(&self) -> usize

The number of rows in the matrix.

fn dot(&self, other: &Self, i: usize, j: usize) -> f32

Compute the dot product between row i of self and row j of other.

fn norm(&self, i: usize) -> f32

Compute the Euclidean norm of row i.

fn auto_correlation(&self, delay: usize) -> f32

Compute the auto-correlation with the given delay.

fn cross_correlation(&self, other: &Self) -> f32

Compute the cross-correlation between two matrices.

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

where A::K: Debug,

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

Formats the value using the given formatter.

impl<A: Alphabet> From<&ScoringMatrix<A>> for DiscreteMatrix<A>

fn from(s: &ScoringMatrix<A>) -> Self

Converts to this type from the input type.

impl<A: Alphabet> From<ScoringMatrix<A>> for DiscreteMatrix<A>

fn from(value: ScoringMatrix<A>) -> Self

Converts to this type from the input type.

impl<A: Alphabet> From<ScoringMatrix<A>> for WeightMatrix<A>

fn from(pwm: ScoringMatrix<A>) -> Self

Converts to this type from the input type.

impl<A: Alphabet> From<WeightMatrix<A>> for ScoringMatrix<A>

fn from(pwm: WeightMatrix<A>) -> Self

Converts to this type from the input type.

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

type Output = <DenseMatrix<f32, <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 ScoringMatrix<A>

where A::K: PartialEq,

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

Tests for self and other values to be equal, and is used by ==.

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

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

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