gv {agvgd}

Grantham variation

Description

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 rho parameter 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.

Value

A numeric vector of grantham variation values.

See Also

gd(), cpv_ranges()

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)