strataG (version 1.0.3)

baseFreqs: Base Frequencies

Description

Calculate nucleotide base frequencies along a sequence.

Usage

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

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 frequencies.

Value

• For each gene, a list containing: ll{ site.freqs a matrix of base frequencies at each site. base.freqs a vector of overall base frequencies. }