Struct TfmPvalue

pub struct TfmPvalue<A: Alphabet, M: AsRef<ScoringMatrix<A>>> { /* private fields */ }

The TFM-PVALUE algorithm.

Implementations

impl<A: Alphabet, M: AsRef<ScoringMatrix<A>>> TfmPvalue<A, M>

pub fn new(matrix: M) -> Self

Initialize the TFM-PVALUE algorithm for the given scoring matrix.

pub fn as_inner(&self) -> &M

Return a reference to the wrapped matrix reference.

pub fn into_inner(self) -> M

Extract the wrapped matrix reference.

pub fn pvalue(&mut self, score: f64) -> f64

Compute the exact P-value for the given score.

Caution

This method internally calls approximate_pvalue without bounds on the granularity, which may require a very large amount of memory for some scoring matrices. Use approximate_pvalue directly to add limits on the number of iterations or on the granularity.

pub fn approximate_pvalue(&mut self, score: f64) -> PvaluesIterator<'_, A, M>

Iterate with decreasing granularity to compute an approximate p-value for a score.

Example

Approximate a p-value for a score of 10.0 with a granularity of 0.001:

// Initialize the TFM-PVALUE algorithm for a lightmotif PSSM
let mut tfmp = lightmotif_tfmpvalue::TfmPvalue::new(&pssm);

// Compute the p-value for a score by iterating
// until granularity or convergence are reached.
let p_value = tfmp.approximate_pvalue(10.0)
    .find(|it| it.converged || it.granularity <= 0.001)
    .map(|it| *it.range.start())
    .unwrap();

pub fn score(&mut self, pvalue: f64) -> f64

Compute the exact score associated with a given p-value.

Caution

This method internally calls approximate_score without bounds on the granularity, which may require a very large amount of memory for some scoring matrices. Use approximate_score directly to add limits on the number of iterations or on the granularity.

pub fn approximate_score(&mut self, pvalue: f64) -> ScoresIterator<'_, A, M>

Iterate with decreasing granularity to compute an approximate score for a p-value.

Trait Implementations

impl<A: Debug + Alphabet, M: Debug + AsRef<ScoringMatrix<A>>> Debug for TfmPvalue<A, M>

where A::K: Debug,

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

Formats the value using the given formatter.

impl<A: Alphabet, M: AsRef<ScoringMatrix<A>>> From<M> for TfmPvalue<A, M>

fn from(matrix: M) -> Self

Converts to this type from the input type.