Description Usage Arguments Details Value Author(s) See Also Examples
This function selects haplotypes based on their (absolute) frequencies and/or proportions of missing nucleotides.
1 2 |
x |
an object of class |
minfreq, maxfreq |
the lower and upper limits of (absolute) haplotype frequencies. By default, all haplotypes are selected whatever their frequency. |
maxna |
the maximum frequency (absolute or relative; see details) of missing nucleotides within a given haplotype. |
na |
a vector of mode character specifying which nucleotide symbols should be treated as missing data; by default, unknown nucleotide (N) and completely unknown site (?) (can be lower- or uppercase). There are two shortcuts: see details. |
... |
unused. |
The value of maxna
can be either less than one, or greater or
equal to one. In the former case, it is taken as specifying the
maximum proportion (relative frequency) of missing data within a given
haplotype. In the latter case, it is taken as the maximum number
(absolute frequency).
na = "all"
is a shortcut for all ambiguous nucleotides
(including N) plus alignment gaps and completely unknown site (?).
na = "ambiguous"
is a shortcut for only ambiguous nucleotides
(including N).
an object of class c("haplotype", "DNAbin")
.
Emmanuel Paradis
1 2 3 4 |
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
/// adegenet 2.0.1 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Attaching package: 'pegas'
The following object is masked from 'package:ade4':
amova
The following object is masked from 'package:ape':
mst
Haplotypes extracted from:
Number of haplotypes: 14
Sequence length: 965
Haplotype labels and frequencies:
I II III IV V VI VII VIII IX X XI XIII XIV XV
1 1 1 1 1 1 1 1 1 1 1 1 1 1
Haplotypes extracted from:
Number of haplotypes: 14
Sequence length: 965
Haplotype labels and frequencies:
I II III IV V VI VII VIII IX X XI XIII XIV XV
1 1 1 1 1 1 1 1 1 1 1 1 1 1
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