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Percent difference Distance

Source: R/P_distance.R
P_distance.Rd

The P-distance is simply the percentage of the aligned base pairs where the two bases are different. See Details for a discussion on the many ways to compute percent identity (and therefore difference.)

The P_error function reports the standard error given the alignment length \(n\) and percent difference \(p\) computed from the matrix: \(\sqrt{p(1 - p) / n}\).

Usage

P_distance(m, denominator = c("L3", "L1", "L2", "L4"))

P_error(m, denominator = c("L3", "L1", "L2", "L4"))

Arguments

m

A matrix of counts (P_distance, P_variance) or probabilities (P_distance only) for bases of the target genome to be aligned to bases on the query genome. As a convenience it can also receive a list produced by the readTrainFile() function, containing this matrix.

denominator

Denominator according to the nomenclature of May (2004). Default is L3.

Value

A numeric value representing the evolutionary distance between two genomes. The larger the value, the more divergent the genomes.

Details

The P-distance is computed as 1 minus the percent sequence identity according to the definitions of May (2004), which is the ratio between the number of matching bases and four possible denominators in use at that time.

  • L1: Length of the shorter sequence.

  • L2: Number of aligned positions, i.e., alignment length (includes gaps, if any).

  • L3: Number of aligned residue pairs, i.e., identities and nonidentities (excludes gaps, if any).

  • L4: Arithmetic mean sequence length.

References

May, A. C. W. (2004). Percent Sequence Identity: The Need to Be Explicit. Structure, 12(5), 737–738. doi:10.1016/j.str.2004.04.001

See also

Other Alignment statistics: F81_distance(), GCequilibrium(), GCpressure(), GCproportion(), HKY85_distance(), JC69_distance(), K80_distance(), T92_distance(), TN93_distance(), exampleSubstitutionMatrix, gapProportion(), logDet_distance()

Other Similarity indexes: F81_distance(), GOC(), HKY85_distance(), JC69_distance(), K80_distance(), T92_distance(), TN93_distance(), correlation_index(), karyotype_index(), logDet_distance(), slidingWindow(), strand_randomisation_index(), synteny_index(), tau_index()

Other Alignment statistics: F81_distance(), GCequilibrium(), GCpressure(), GCproportion(), HKY85_distance(), JC69_distance(), K80_distance(), T92_distance(), TN93_distance(), exampleSubstitutionMatrix, gapProportion(), logDet_distance()

Author

Charles Plessy

Examples

P_distance(exampleSubstitutionMatrix)
#> [1] 0.2312837

# example code
P_error(exampleSubstitutionMatrix)
#> [1] 7.701531e-05