This function calculates the Grantham variation (\(\mathrm{gv}\)):
$$\mathrm{gv} = \rho \left((\alpha (c_{max}-c_{min})^2 + \beta (p_{max}-p_{min})^2 + \gamma (v_{max}-v_{min})^2\right)^\frac{1}{2}$$
The minimum and maximum values are those observed for a set of amino acid residues at the alignment position of interest.
Usage
gv(
c_min,
c_max,
p_min,
p_max,
v_min,
v_max,
alpha = 1.833,
beta = 0.1018,
gamma = 0.000399,
rho = 50.723
)Arguments
- c_min
Amino acid composition, minimum value.
- c_max
Amino acid, composition, maximum value.
- p_min
Amino acid polarity, minimum value.
- p_max
Amino acid polarity, maximum value.
- v_min
Amino acid molecular volume, maximum value.
- v_max
Amino acid molecular volume, maximum value.
- alpha
The constant \(\alpha\) in Grantham's equation. It is the square inverse of the mean of the composition property.
- beta
The constant \(\beta\) in Grantham's equation. It is the square inverse of the mean of the polarity property.
- gamma
The constant \(\gamma\) in Grantham's equation. It is the square inverse of the mean of the molecular volume property.
- rho
Grantham's distances reported in Table 2, Science (1974). 185(4154): 862--4 by R. Grantham, are scaled by a factor (here named \(\rho\)) such that the mean value of all distances are 100. The
rhoparameter allows this factor \(\rho\) to be changed. By default \(\rho=50.723\), the same value used by Grantham. This value is originally mentioned in the caption of Table 2 of the aforementioned paper.