Benchmarking Secondary Structure Predictions
Typedefs
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typedef struct vrna_score_s vrna_score_t
Typename for the score data structure vrna_score_s.
#include <ViennaRNA/structures/benchmark.h>
Functions
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vrna_score_t vrna_score_from_confusion_matrix(int TP, int TN, int FP, int 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
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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
- 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
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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
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struct vrna_score_s
- #include <ViennaRNA/structures/benchmark.h>
The data structure that contains statistic result of two structures comparaison.
Public Members
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int TP
True Positive count.
#include <ViennaRNA/structures/benchmark.h>
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int TN
True Negative count.
#include <ViennaRNA/structures/benchmark.h>
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int FP
False Positive count.
#include <ViennaRNA/structures/benchmark.h>
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int FN
False Negative count.
#include <ViennaRNA/structures/benchmark.h>
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float TPR
True Positive Rate.
#include <ViennaRNA/structures/benchmark.h>
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float PPV
Positive Predictive Value.
#include <ViennaRNA/structures/benchmark.h>
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float FPR
False Positive Rate.
#include <ViennaRNA/structures/benchmark.h>
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float FOR
False Omission Rate.
#include <ViennaRNA/structures/benchmark.h>
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float TNR
True Negative Rate.
#include <ViennaRNA/structures/benchmark.h>
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float FDR
False Discovery Rate.
#include <ViennaRNA/structures/benchmark.h>
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float FNR
False Negative Rate.
#include <ViennaRNA/structures/benchmark.h>
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float NPV
Negative Predictive Value.
#include <ViennaRNA/structures/benchmark.h>
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float F1
F1 Score.
#include <ViennaRNA/structures/benchmark.h>
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float MCC
Matthews Correlation Coefficient.
#include <ViennaRNA/structures/benchmark.h>
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int TP
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typedef struct vrna_score_s vrna_score_t