solveAmbiguousBases: Solve Ambiguous Bases in DNA Sequences

In ape: Analyses of Phylogenetics and Evolution

Solve Ambiguous Bases in DNA Sequences

Description

Replaces ambiguous bases in DNA sequences (R, Y, W, ...) by A, G, C, or T.

Usage

solveAmbiguousBases(x, method = "columnwise", random = TRUE)

Arguments

x	a matrix of class "DNAbin"; a list is accepted and is converted into a matrix.
method	the method used (no other choice than the default for the moment; see details).
random	a logical value (see details).

Details

The replacements of ambiguous bases are done columwise. First, the base frequencies are counted: if no ambiguous base is found in the column, nothing is done. By default (i.e., if random = TRUE), the replacements are done by random sampling using the frequencies of the observed compatible, non-ambiguous bases. For instance, if the ambiguous base is Y, it is replaced by either C or T using their observed frequencies as probabilities. If random = FALSE, the greatest of these frequencies is used. If there are no compatible bases in the column, equal probabilities are used. For instance, if the ambiguous base is R, and only C and T are observed, then it is replaced by either A or G with equal probabilities.

Alignment gaps are not changed; see the function latag2n to change the leading and trailing gaps.

Value

a matrix of class "DNAbin".

Author(s)

Emmanuel Paradis

See Also

base.freq, latag2n, dnds

Examples

X <- as.DNAbin(matrix(c("A", "G", "G", "R"), ncol = 1))
alview(solveAmbiguousBases(X)) # R replaced by either A or G
alview(solveAmbiguousBases(X, random = FALSE)) # R always replaced by G

ape documentation built on March 31, 2023, 6:56 p.m.