Tidy genind object from adegenet to a tidy dataframe. Used internally in radiator and might be of interest for users.
tidy_genind(data, tidy = TRUE, gds = TRUE, write = FALSE, verbose = FALSE)(path or object) A genind object in the global environment or
path to a genind file that will be open with readRDS.
(logical) Generate a tidy dataset.
Default: tidy = TRUE.
(optional, logical) To write a radiator gds object.
Currently, for biallelic datasets only.
Default: gds = TRUE.
(optional, logical) To write in the working directory the tidy
data. The file is written with radiator_genind_DATE@TIME.rad.
Default: write = FALSE.
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE.
genind objects, like
genepop, are not optimal genomic format for RADseq datasets,
they lack important genotypes and markers metadata: chromosome, locus, snp,
position, read depth, allele depth, etc.
genlight object is a more
interesting container and is memory efficient, see tidy_genlight.
By default allele names will be kept for the tidy dataset, if the alleles is numeric and length < 3.
In the unlikely event that the genind object as no stratification/population, pop will be added to the strata column.
Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.
Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics, 27, 3070-3071.