env.sp: Extract the Sequence Environments

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Extracts the sequence environments around the selected amino acid(s) in the chosen species.

Usage

env.sp(data, sp, r = 10, aa = 'all', silent = TRUE)

Arguments

data	input data must be a dataframe (see details).
sp	the species of interest (it should be named as in the input dataframe).
r	a positive integer indicating the radius of the sequence segment considered as environment.
aa	the amino acid(s) which environments are going to be extracted.
silent	logical. When FALSE the program progress is reported to alleviate loneliness.

Details

Input data must be a dataframe where each row corresponds to an individual protein. The columns contain the sequence of the protein corresponding to the row in each species. Therefore, the columns' names of this dataframe must be coherent with the names of the OTUs being analyzed.

Value

A list of environment sequences. Each element from the list is a vector with the environment sequences around an amino acid. So, the length list is the same as the length of aa.

See Also

otu.vector(), otu.space()

Examples

data(bovids)
env.sp(data = bovids, sp = "Bos_taurus", r = 2)

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.