checkDNA: Check a DNA alignment for missing data
In boopsboops/spider: Species Identity and Evolution in R
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
This functions counts the number of bases in an alignment that are composed
of missing data.
Usage
1
Arguments
DNAbin
A DNA alignment of class ‘DNAbin’.
gapsAsMissing
Logical. Should gaps (coded as '-') be considered
missing bases? Default of TRUE.
Details
This function considers bases coded as '?' and 'N' as missing data. By
default, gaps (coded as '-') are also considered missing.
Value
A numeric vector giving the number of missing bases in each sequence
of the alignment.
Author(s)
Samuel Brown <[email protected]>
Examples
1
2
3
data(anoteropsis)
checkDNA(anoteropsis)
checkDNA(anoteropsis, gapsAsMissing=FALSE)
boopsboops/spider documentation built on May 6, 2019, 8:49 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
This functions counts the number of bases in an alignment that are composed of missing data.
Usage
1 |
Arguments
DNAbin |
A DNA alignment of class ‘DNAbin’. |
gapsAsMissing |
Logical. Should gaps (coded as '-') be considered missing bases? Default of TRUE. |
Details
This function considers bases coded as '?' and 'N' as missing data. By default, gaps (coded as '-') are also considered missing.
Value
A numeric vector giving the number of missing bases in each sequence of the alignment.
Author(s)
Samuel Brown <[email protected]>
Examples
1 2 3 | data(anoteropsis)
checkDNA(anoteropsis)
checkDNA(anoteropsis, gapsAsMissing=FALSE)
|
boopsboops/spider documentation built on May 6, 2019, 8:49 a.m.
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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