Compare RNA secondary structure by their confusion matrix. More...

#include <confusion_matrix.hh>

Classes
class	BPFilter
	basic class for base pair filters (no filtering) More...

class	BPMinLoopSizeFilter
	loop size base pair filter More...

class	CanonicalBPFilter
	base pair filter to allow only canonical base pairs More...

class	CombinedBPFilter

class	SpanRangeBPFilter
	base pair range filter More...

Public Types
typedef std::pair< size_t, size_t >	bp_t

Public Member Functions
	ConfusionMatrix (const std::string &ref, const std::string &pred, const bool slide, const bool conflict, const BPFilter &filter=BPMinLoopSizeFilter(3))

	ConfusionMatrix (const RnaStructure &ref, const RnaStructure &pred, const bool slide, const bool conflict, const BPFilter &filter=BPMinLoopSizeFilter(3))

size_t	tp () const
	True positives. More...

size_t	tn () const
	True negatives. More...

size_t	fp () const
	False positives. More...

size_t	fn () const

double	ppv () const

double	sens () const

double	spec () const

double	f1_score () const

double	mcc () const

Protected Member Functions
size_t	count_common_bps (const RnaStructure &s1, const RnaStructure &s2)
	Count common base pairs. More...

size_t	count_tps (const RnaStructure &pred, const RnaStructure &ref)
	Count true positive base pairs. More...

size_t	count_conflicting_base_pairs (const RnaStructure &s1, const RnaStructure &s2)
	Count conflicting base pairs (including common bps) More...

size_t	count_potential_base_pairs (size_t length)
	Count potential base pairs. More...

size_t	count_base_pairs (const RnaStructure &s)
	Count base pairs in a structure. More...

Detailed Description

Compare RNA secondary structure by their confusion matrix.

Computes confusion matrix and Matthews' correlation coefficient

Base pair filters provide a generic way to count only a subset of potential base pairs, e.g. only canonical base pairs, or base pairs in a certain range l..u

Implements slide rule and conflict rule; see Paul special

Slide rule: tolerate shift of one base pair end by 1 position (affects true positives and false negatives)

Conflict rule: predicted base pairs are false only if they conflict with reference; two base pair conflict iff they share one end (affects "false positives")

Member Typedef Documentation

typedef std::pair<size_t,size_t> LocARNA::ConfusionMatrix::bp_t

type of a base pair

Constructor & Destructor Documentation

LocARNA::ConfusionMatrix::ConfusionMatrix	(	const std::string &	ref,
		const std::string &	pred,
		const bool	slide,
		const bool	conflict,
		const BPFilter &	filter = `BPMinLoopSizeFilter(3)`
	)

Construct with reference and predicted structure (given as dot-bracket strings)

Parameters

ref	reference structure
pred	predicted structure
slide	use slide rule [default off]
conflict	use conflict rule [default off]
filter	base pair filter

LocARNA::ConfusionMatrix::ConfusionMatrix	(	const RnaStructure &	ref,
		const RnaStructure &	pred,
		const bool	slide,
		const bool	conflict,
		const BPFilter &	filter = `BPMinLoopSizeFilter(3)`
	)

Construct with reference and predicted structure (given as base pair sets)

Parameters

ref	reference structure
pred	predicted structure
slide	use slide rule [default off]
conflict	use conflict rule [default off]
filter	base pair filter

Member Function Documentation

size_t LocARNA::ConfusionMatrix::count_base_pairs ( const RnaStructure & s )

protected

Count base pairs in a structure.

Parameters

structure RNA structure

Returns: number of base pairs

size_t LocARNA::ConfusionMatrix::count_common_bps	(	const RnaStructure &	s1,
		const RnaStructure &	s2
	)

protected

Count common base pairs.

Parameters

s1	first structure
s2	second structure

Returns: number of base pairs in the first structure that are as well in the second (optionally according to slide rule)

Note: due to slide rule this is not symmetric

size_t LocARNA::ConfusionMatrix::count_conflicting_base_pairs	(	const RnaStructure &	s1,
		const RnaStructure &	s2
	)

protected

Count conflicting base pairs (including common bps)

Parameters

s1	first structure
s2	second structure

Two base pairs (i,j) and (i',j') conflict if and only if they share exactly one end.

Returns: number of base pairs in s1 that conflict with s2

size_t LocARNA::ConfusionMatrix::count_potential_base_pairs ( size_t length )

protected

Count potential base pairs.

Parameters

length length of RNA

Returns: number of potential base pairs

size_t LocARNA::ConfusionMatrix::count_tps	(	const RnaStructure &	pred,
		const RnaStructure &	ref
	)

protected

Count true positive base pairs.

Parameters

pred	predicted structure
ref	reference structure

Returns: number of true positive base pairs

double LocARNA::ConfusionMatrix::f1_score ( ) const

F1 score (aka F-score, F-measure)

harmonic mean of PPV and SENS

Returns: F1 = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise

size_t LocARNA::ConfusionMatrix::fn ( ) const

inline

False negatives

Returns: number of false negative base pairs

Note: A false negative is pair annotated to basepair but not predicted.

size_t LocARNA::ConfusionMatrix::fp ( ) const

inline

False positives.

Returns: number of false positive base pairs

Note: A false positive is a pair predicted to basepair but not annotated.

double LocARNA::ConfusionMatrix::mcc ( ) const

Matthews' correlation coefficient

Returns: MCC = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) )

double LocARNA::ConfusionMatrix::ppv ( ) const

Positive prediction value

aka precision

Returns: PPV = TP/(TP+FP)

double LocARNA::ConfusionMatrix::sens ( ) const

Sensitivity

aka recall

Returns: SENS = TP/(TP+FN)

double LocARNA::ConfusionMatrix::spec ( ) const

Specificity

Returns: SPEC = TN/(TN+FP)

size_t LocARNA::ConfusionMatrix::tn ( ) const

inline

True negatives.

Returns: number of true negative base pairs

Note: A true negative is a pair which is neither annotated nor predicted to basepair

size_t LocARNA::ConfusionMatrix::tp ( ) const

inline

True positives.

Returns: number of true positive base pairs

Note: A true positive is a pair that is basepaired in both prediction and annotation; this is softened with slide rule, see ().

The documentation for this class was generated from the following files:

src/LocARNA/confusion_matrix.hh
src/LocARNA/confusion_matrix.cc

Classes

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation