gd: Grantham deviation

In agvgd: An R Implementation of the 'Align-GVGD' Method

Grantham deviation

Description

This function calculates the Grantham deviation (\mathrm{gd}):

\mathrm{gd} = ρ ≤ft((α\ \mathrm{dev}^2(c_x, c_{min}, c_{max}) + β\ \mathrm{dev}^2(p_x, p_{min}, p_{max}) + γ\ \mathrm{dev}^2(v_x, v_{min}, v_{max})\right)^\frac{1}{2}

where c_x is the value for composition c of amino acid x, i.e. the atomic weight ratio of hetero (noncarbon) elements in end groups or rings to carbons in the side chain; p_x is the value for polarity p of amino acid x; and, v_x is the value for molecular volume v of amino acid x.

c_x, p_x and v_x are looked up in grantham::amino_acids_properties based on the amino acid identities passed in x. The function \mathrm{dev} is implemented in dev(). Remaining variables in the equation are arguments to gd() and hence are explained below in the Arguments section.

Usage

gd(
  x,
  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

x	A character vector of one-letter amino acid codes, indicating missense substitutions.
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 deviations. Each deviation corresponds to one of the amino acids indicated in x.

See Also

gv(), dev()

Examples

gd('S', c_min = 0.39, c_max = 0.74, p_min =4.9, p_max =8.6, v_min = 3, v_max = 32.5)

agvgd documentation built on Sept. 11, 2022, 1:07 a.m.