is.ambig {spider} | R Documentation |
Missing bases in alignments
Description
Checks what columns in an alignment have ambiguous bases or missing data.
Usage
is.ambig(DNAbin)
Arguments
DNAbin |
A DNA alignment of class ‘DNAbin’. |
Details
Ambiguous bases are bases that have been coded with any of the Union of Pure and Applied Chemistry (IUPAC) DNA codes that are not A, C, G, or T. Missing data are bases that have been coded with "-", "?" or "N".
Value
A logical vector containing TRUE if ambiguous bases or missing data are present, FALSE if not. Does not differentiate between the two classes of data.
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
See Also
Examples
data(woodmouse)
is.ambig(woodmouse)
#Columns with ambiguous bases
which(is.ambig(woodmouse))
[Package spider version 1.5.0 Index]