adegenet (version 1.2-3)

SequencesToGenind: 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

encoding

UTF-8

See Also

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

Examples

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