subset.haplotype: Subsetting and Filtering Haplotypes

In pegas: Population and Evolutionary Genetics Analysis System

Description

This function selects haplotypes based on their (absolute) frequencies and/or proportions of missing nucleotides.

Usage

## S3 method for class 'haplotype'
subset(x, minfreq = 1, maxfreq = Inf, maxna = Inf, na = c("N", "?"), ...)

Arguments

x	an object of class c("haplotype", "DNAbin").
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.

Details

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).

Value

an object of class c("haplotype", "DNAbin").

Author(s)

Emmanuel Paradis

See Also

haplotype

Examples

data(woodmouse)
h <- haplotype(woodmouse)
subset(h, maxna = 20)
subset(h, maxna = 20/ncol(h)) # same thing than above

Example output

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 

pegas documentation built on Dec. 16, 2021, 5:09 p.m.