Importing data from an alignement of sequences to a genind object
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
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)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 |
polyThres |
the minimum frequency of a minor allele for a locus to be considered as polymorphic (defaults to 0.01). |
an object of the class genind
Thibaut Jombart t.jombart@imperial.ac.uk
## 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-")
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