genind2df: Convert a genind object to a data.frame.

In skayondo/adegenet: Exploratory Analysis of Genetic and Genomic Data

Description

The function genind2df converts a genind back to a data.frame of raw allelic data.

Usage

genind2df(x, pop = NULL, sep = "", usepop = TRUE, oneColPerAll = FALSE)

Arguments

x	a genind object
pop	an optional factor giving the population of each individual.
sep	a character string separating alleles. See details.
usepop	a logical stating whether the population (argument pop or x@pop should be used (TRUE, default) or not (FALSE)).
oneColPerAll	a logical stating whether or not alleles should be split into columns (defaults to FALSE). This will only work with data with consistent ploidies.

Value

a data.frame of raw allelic data, with individuals in rows and loci in column

Author(s)

Thibaut Jombart [e-mail]

See Also

df2genind, import2genind, read.genetix, read.fstat, read.structure

Examples

## simple example
df <- data.frame(locusA=c("11","11","12","32"),
locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
row.names(df) <- .genlab("genotype",4)
df

obj <- df2genind(df, ploidy=2, ncode=1)
obj
obj@tab


## converting a genind as data.frame
genind2df(obj)
genind2df(obj, sep="/")

skayondo/adegenet documentation built on July 18, 2020, 12:38 a.m.