Computes the following equation: $$\frac{\text{W}\to\text{S} \quad-\quad \text{S}\to\text{W}}{\text{W}\to\text{S} \quad+\quad \text{S}\to\text{W}}$$
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.
Note
This index was suggested to by by M365 Copilot while using it to write
the GCequilibrium function and its documentation. Despite my attempts I
could not find a paper that uses it explicitely… I am including it in this
package because I am screening as many indices that I can extract from an
alignment pair.
See also
Other Alignment statistics:
F81_distance(),
GCequilibrium(),
GCproportion(),
JC69_distance(),
K80_distance(),
P_distance(),
T92_distance(),
exampleSubstitutionMatrix,
gapProportion()
Examples
GCpressure(exampleSubstitutionMatrix)
#> [1] 0.02888339
GCpressure(t(exampleSubstitutionMatrix))
#> [1] -0.02888339