SequencesToGenind {adegenet}R Documentation

Importing data from an alignement of sequences to a genind object

Description

These functions take an alignement of sequences and translate SNPs into a genind object. Note that only polymorphic loci are retained.

Currently, accepted sequence formats are:
- DNAbin (ape package): function DNAbin2genind
- alignement (seqinr package): to come...

Usage

DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char=NULL, polyThres=1/100)

Arguments

x an object containing aligned sequences.
pop an optional factor giving the population to which each sequence belongs.
exp.char a vector of single character providing expected values; all other characters will be turned to NA.
na.char a vector of single characters providing values that should be considered as NA. If not NULL, this is used instead of exp.char.
polyThres the minimum frequency of a minor allele for a locus to be considered as polymorphic (defaults to 0.01).

Value

an object of the class genind

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

See Also

import2genind, read.genetix, read.fstat, read.structure, read.genepop, DNAbin.

Examples

if(require(ape)){
data(woodmouse)
x <- DNAbin2genind(woodmouse)
x
genind2df(x)
}

[Package adegenet version 1.2-3 Index]