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

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
- 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 t.jombart@imperial.ac.uk

### 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-")

    }

[Package adegenet version 2.1.4 Index]