tidy_genind: Tidy a genind object to a tidy dataframe

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Tidy a genind object to a tidy dataframe

Description

Tidy genind object from adegenet to a tidy dataframe. Used internally in radiator and might be of interest for users.

Usage

tidy_genind(data, tidy = TRUE, gds = TRUE, write = FALSE, verbose = FALSE)

Arguments

data	(path or object) A genind object in the global environment or path to a genind file that will be open with readRDS.
tidy	(logical) Generate a tidy dataset. Default: tidy = TRUE.
gds	(optional, logical) To write a radiator gds object. Currently, for biallelic datasets only. Default: gds = TRUE.
write	(optional, logical) To write in the working directory the tidy data. The file is written with [e-mail]. Default: write = FALSE.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

Note

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.

Author(s)

Thierry Gosselin [e-mail]

References

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.

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.