is.ambig: Missing bases in alignments
In boopsboops/spider: Species Identity and Evolution in R
is.ambig 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
checkDNA
Examples
data(woodmouse)
is.ambig(woodmouse)
#Columns with ambiguous bases
which(is.ambig(woodmouse))
boopsboops/spider documentation built on June 2, 2025, 7:28 a.m.
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| is.ambig | 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
checkDNA
Examples
data(woodmouse)
is.ambig(woodmouse)
#Columns with ambiguous bases
which(is.ambig(woodmouse))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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