Convert Data to genind Format
This is a function for exporting data to the package adegenet.
gendata.to.genind(object, samples = Samples(object), loci = Loci(object))
object |
A |
samples |
A character vector indicating the samples to include in the output. |
loci |
A character vector indicating the loci to include in the output. |
gendata.to.genind converts a "genambig" or
"genbinary" object to a "genind" object using the package
adegenet. Each individual must have a single ploidy.
Ploidy and population information are carried over to the new
object. Data will be coded as presence/absence in the new object. The
locus names in the new object are locus and allele names
seperated by a hyphen.
adegenet must be installed in order to use this function.
A genetic dataset in the "genind" class, ready for use in
adegenet.
Lindsay V. Clark
Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405.
# create a "genambig" object
mydata <- new("genambig", samples=c("a","b","c","d"), loci=c("e","f"))
PopNames(mydata) <- c("G","H")
PopInfo(mydata) <- c(1,1,2,2)
mydata <- reformatPloidies(mydata, output="one")
Ploidies(mydata) <- 3
Genotypes(mydata, loci="e") <- list(c(100),c(100,102),
c(98,102,104),c(102,106))
Genotypes(mydata, loci="f") <- list(c(200,202,204),Missing(mydata),
c(210,212),c(204,210,214))
# convert to "genind"
if(require("adegenet")){
mydata2 <- gendata.to.genind(mydata)
mydata2@tab
locNames(mydata2)
indNames(mydata2)
popNames(mydata2)
pop(mydata2)
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