This function calculates the Grantham variation (gv):
gv=ρ((α(cmax−cmin)2+β(pmax−pmin)2+γ(vmax−vmin)2)12
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 α in Grantham's equation. It is the square inverse of the mean of the composition property.
- beta
The constant β in Grantham's equation. It is the square inverse of the mean of the polarity property.
- gamma
The constant γ 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 ρ) such that the mean value of all distances are 100. The
rho
parameter allows this factor ρ to be changed. By default ρ=50.723, the same value used by Grantham. This value is originally mentioned in the caption of Table 2 of the aforementioned paper.