Proportion of GC in alignment

The proportion of GC in the target genome in an alignment. For the same on the query genome, just transpose the input matrix.

Usage

GCproportion(m)

Arguments

m

A matrix of counts or probabilities 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.

Value

A numeric value between 0 and 1.

See also

Other Alignment statistics: F81_distance(), GCequilibrium(), GCpressure(), JC69_distance(), K80_distance(), P_distance(), T92_distance(), exampleSubstitutionMatrix, gapProportion()

Author

Charles Plessy

Examples

GCproportion(exampleSubstitutionMatrix)
#> [1] 0.4347341
GCproportion(t(exampleSubstitutionMatrix))
#> [1] 0.4302136