Benchmarking Secondary Structure Predictions

Typedefs

typedef struct vrna_score_s vrna_score_t

Typename for the score data structure vrna_score_s. 

#include <ViennaRNA/structures/benchmark.h>

Functions

vrna_score_t vrna_score_from_confusion_matrix(double TP, double TN, double FP, double FN)

Construct score data structure from given confusion matrix. 

#include <ViennaRNA/structures/benchmark.h>
Parameters:

  • TP – True positive count

  • TN – True negative count

  • FP – False positive count

  • FN – False negative count

Returns:

The score data structure to write

vrna_score_t vrna_compare_structure_pt(const short *pt_gold, const short *pt_other, int fuzzy)

Return statistic of two structure (in pair table) comparaison. 

#include <ViennaRNA/structures/benchmark.h>

See also

vrna_compare_structure

Parameters:

  • pt_gold – Gold standard structure in pair table

  • pt_other – Structure to compare in pair table

  • fuzzy – Allows for base pair slippage. Hence, for any base pair (i,j) in the gold standard, a base pair (p, q) in the second structure is considered a true positive, if i - fuzzy <= p <= i + fuzzy, and j - fuzzy <= q <= j + fuzzy.

Returns:

The vrna_score_s data structure

vrna_score_t vrna_compare_structure(const char *structure_gold, const char *structure_other, int fuzzy, unsigned int options)

Return statistic of two structure (in dbn) comparaison. 

#include <ViennaRNA/structures/benchmark.h>
Parameters:

  • pt_gold – Gold standard structure

  • pt_other – Structure to compare

  • fuzzy – Allows for base pair slippage. Hence, for any base pair (i,j) in the gold standard, a base pair (p, q) in the second structure is considered a true positive, if i - fuzzy <= p <= i + fuzzy, and j - fuzzy <= q <= j + fuzzy.

  • options – A bitmask to specify which brackets are recognized during conversion to pair table

Returns:

The vrna_score_s data structure

struct vrna_score_s
#include <ViennaRNA/structures/benchmark.h>

The data structure that contains statistic result of two structures comparaison.

Public Members

double TP

True Positive count. 

#include <ViennaRNA/structures/benchmark.h>
double TN

True Negative count. 

#include <ViennaRNA/structures/benchmark.h>
double FP

False Positive count. 

#include <ViennaRNA/structures/benchmark.h>
double FN

False Negative count. 

#include <ViennaRNA/structures/benchmark.h>
double TPR

True Positive Rate. 

#include <ViennaRNA/structures/benchmark.h>
double PPV

Positive Predictive Value. 

#include <ViennaRNA/structures/benchmark.h>
double FPR

False Positive Rate. 

#include <ViennaRNA/structures/benchmark.h>
double FOR

False Omission Rate. 

#include <ViennaRNA/structures/benchmark.h>
double TNR

True Negative Rate. 

#include <ViennaRNA/structures/benchmark.h>
double FDR

False Discovery Rate. 

#include <ViennaRNA/structures/benchmark.h>
double FNR

False Negative Rate. 

#include <ViennaRNA/structures/benchmark.h>
double NPV

Negative Predictive Value. 

#include <ViennaRNA/structures/benchmark.h>
double F1

F1 Score. 

#include <ViennaRNA/structures/benchmark.h>
double MCC

Matthews Correlation Coefficient. 

#include <ViennaRNA/structures/benchmark.h>