otu.vector {EnvNJ}

Convert a Set of Sequence Environments into a Vector

Description

Converts a set of sequence environments into a vector.

Usage

otu.vector(envl, sp = "", aa = "all", silent = TRUE)

Arguments

envl

a list containing the sequence environment of a species (as the one returned by the function env.sp()).

sp

character string indicating the species being analyzed.

aa

the amino acid(s) to be used to encoded the species.

silent

logical. When FALSE the program progress is reported to alleviate loneliness.

Details

The dimension of the vector representing the species will depend on the settings. For instance, if we choose a single amino acid and a radius of 10 for the sequence environment, then we will get a vector of dimension 400 (20 amino acids x 20 positions). If we opt for the 20 amino acids and r = 10, then the vector will be of dimension 8000 (400 for each amino acid * 20 amino acids). Please, note that r is selected in the function env.sp() that will provide the input dataframe for the current function.

Value

A matrix representing the species. This matrix can be converted into a vector representing the target species just typing as.vector(matrix). Each coordinate is the frequency of a given amino acid at a certain position from the environment (see details).

See Also

env.sp(), otu.space()

Examples

data(bovids)
cow = env.sp(bovids, "Bos_taurus")
otu.vector(cow)