Benchmarking Secondary Structure Predictions — ViennaRNA Package

# 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>