adegenet: hybridize – R documentation

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hybridize

Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.

Description

The function hybridize performs hybridization between two set of genotypes stored in genind objects (referred as the "2 populations"). Allelic frequencies are derived for each population, and then gametes are sampled following a multinomial distribution.

Usage

hybridize(
  x1,
  x2,
  n,
  pop = "hybrid",
  res.type = c("genind", "df", "STRUCTURE"),
  file = NULL,
  quiet = FALSE,
  sep = "/",
  hyb.label = "h"
)

Arguments

`x1`	a genind object
`x2`	a genind object
`n`	an integer giving the number of hybrids requested
`pop`	a character string giving naming the population of the created hybrids.
`res.type`	a character giving the type of output requested. Must be "genind" (default), "df" (i.e. data.frame like in `genind2df`), or "STRUCTURE" to generate a .str file readable by STRUCTURE (in which case the 'file' must be supplied). See 'details' for STRUCTURE output.
`file`	a character giving the name of the file to be written when 'res.type' is "STRUCTURE"; if NULL, a the created file is of the form "hybrids\_[the current date].str".
`quiet`	a logical specifying whether the writing to a file (when 'res.type' is "STRUCTURE") should be announced (FALSE, default) or not (TRUE).
`sep`	a character used to separate two alleles
`hyb.label`	a character string used to construct the hybrids labels; by default, "h", which gives labels: "h01", "h02", "h03",...

Details

The result consists in a set of 'n' genotypes, with different possible outputs (see 'res.type' argument).

If the output is a STRUCTURE file, this file will have the following caracteristics:
- file contains the genotypes of the parents, and then the genotypes of hybrids
- the first column identifies genotypes
- the second column identifies the population (1 and 2 for parents x1 and x2; 3 for hybrids)
- the first line contains the names of the markers
- one row = one genotype (onerowperind will be true)
- missing values coded by "-9" (the software's default)

Value

A genind object (by default), or a data.frame of alleles (res.type="df"). No R output if res.type="STRUCTURE" (results written to the specified file).

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

## Not run: 
## Let's make some cattle hybrids
data(microbov)

## first, isolate each breed
temp <- seppop(microbov)
names(temp)
salers <- temp$Salers
zebu <- temp$Zebu

## let's make some... Zeblers
zebler <- hybridize(salers, zebu, n=40,
                    pop="Zebler")


## now let's merge all data into a single genind
newDat <- repool(microbov, zebler)

## make a correspondance analysis
## and see where hybrids are placed
X <- genind2genpop(newDat, quiet=TRUE)
coa1 <- dudi.coa(tab(X),scannf=FALSE,nf=3)
s.label(coa1$li)
add.scatter.eig(coa1$eig,2,1,2)


## End(Not run)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release