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This function calculates the Grantham variation (gv):

gv=ρ((α(cmaxcmin)2+β(pmaxpmin)2+γ(vmaxvmin)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.

Value

A numeric vector of grantham variation values.

See also

Examples

# Example based on values from Figure 1C of Tavtigian et al. (2006),
# https://doi.org/10.1136/jmg.2005.033878.
gv(c_min = 0, c_max = 0, p_min = 5.7, p_max = 4.9, v_min = 132, v_max = 105)
#> [1] 30.26523