sequences: Importing data from an alignement of sequences to a genind...

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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
- alignment (seqinr package): function alignment2genind

Usage

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

alignment2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-",
                 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 [e-mail]

See Also

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

Examples

## Not run: 
data(woodmouse)
x <- DNAbin2genind(woodmouse)
x
genind2df(x)

## End(Not run)

if(require(seqinr)){
mase.res   <- read.alignment(file=system.file("sequences/test.mase",package="seqinr"),
format = "mase")
mase.res
x <- alignment2genind(mase.res)
x
locNames(x) # list of polymorphic sites
genind2df(x)

## look at Euclidean distances
D <- dist(tab(x))
D

## summarise with a PCoA
pco1 <- dudi.pco(D, scannf=FALSE,nf=2)
scatter(pco1, posi="bottomright")
title("Principal Coordinate Analysis\n-based on proteic distances-")

}

adegenet documentation built on Feb. 16, 2023, 6 p.m.