solveAmbiguousBases {ape} | R Documentation |
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 |
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
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