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NCBI C++ ToolKit: src/algo/blast/composition_adjustment/unified_pvalues.c File Reference

Procedures for computing a "composition" p-value of a match, and for computing a unified p-value combining the customary alignment p-value and the new composition p-value. More...

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static double  P_lambda_table [565]   P_lambda_table is a discretized version of the empirical cumulative distribution function for the statistical parameter lambda for pairs of unrelated sequences in the Astral data set. More...
 

Procedures for computing a "composition" p-value of a match, and for computing a unified p-value combining the customary alignment p-value and the new composition p-value.

Definition in file unified_pvalues.c.

◆ LAMBDA_BIN_SIZE #define LAMBDA_BIN_SIZE   0.001

bin size when discretizing lambda distribution function

Definition at line 48 of file unified_pvalues.c.

◆ LAMBDA_BIN_TOTAL #define LAMBDA_BIN_TOTAL   565

total number of bins for the lambda distribution function

Definition at line 50 of file unified_pvalues.c.

◆ LENGTH_MAX ◆ LENGTH_MIN

The next two constants are used as thresholds in one test of whether to use compositional p-values

Definition at line 43 of file unified_pvalues.c.

◆ LOW_LAMBDA_BIN_CUT #define LOW_LAMBDA_BIN_CUT   35

Marks the boundary of the left tail of the lambda distribution; values of lambda that lie in the left tail are treated all same.

Definition at line 53 of file unified_pvalues.c.

◆ Blast_CompositionPvalue() double Blast_CompositionPvalue ( double  lambda ) ◆ Blast_Overall_P_Value() double Blast_Overall_P_Value ( double  p_comp, double  p_alignment  )

This function implements the method of Fisher, R.

C. Elston (1991) Biometrical J. 33:339-345 and T. L. Bailey and M. Gribskov (1998) Bioinformatics 14:48-54. to combine to p-values into a unified p-value. The input p-values are p_comp and p_alignment. The value returned, call it p_return, is the area in the unit square under the curve y = p_comp*p_align.

Parameters
p_comp composition p-value p_alignment alignment p-value

Definition at line 245 of file unified_pvalues.c.

References log.

Referenced by s_AdjustEvaluesForComposition().

◆ P_lambda_table double P_lambda_table[565] static

P_lambda_table is a discretized version of the empirical cumulative distribution function for the statistical parameter lambda for pairs of unrelated sequences in the Astral data set.

Definition at line 61 of file unified_pvalues.c.

Referenced by Blast_CompositionPvalue().

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