baseFreqs: Base Frequencies

In strataG: Summaries and Population Structure Analyses of Genetic Data

Description

Calculate nucleotide base frequencies along a sequence.

Usage

baseFreqs(x, bases = NULL, ignore = c("n", "x", "-", "."), simplify = TRUE)

Arguments

x	a gtypes object with aligned sequences or a list of aligned DNA sequences.
bases	character vector of bases. Must contain valid IUPAC codes. If NULL, will return summary of frequencies of observed bases.
ignore	a character vector of bases to ignore when calculating site frequencies.
simplify	if there is a single locus, return result in a simplified form? If FALSE a list will be returned wth one element per locus.

Value

For each gene, a list containing:

site.freqs	a matrix of base frequencies at each site.
base.freqs	a vector of overall base proportion composition.

Author(s)

Eric Archer [e-mail]

Examples

data(dloop.g)
bf <- baseFreqs(dloop.g)

# Frequencies of first 10 sites
bf$site.freqs[, 1:10]

# Base composition
bf$base.freqs

strataG documentation built on Feb. 28, 2020, 9:07 a.m.