hybridize {adegenet} | R Documentation |
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.
The result consists in a set of 'n' genotypes, with different possible outputs (see 'res.type' argument).
hybridize(x1, x2, n, pop=NULL, res.type=c("genind","df","STRUCTURE"), file=NULL, quiet=FALSE, sep="/", hyb.label="h")
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. If NULL, will have the form "x1-x2" |
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",... |
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)
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).
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
## Let's make some cattle hybrids ## data(microbov) ## first, isolate each breed temp <- seppop(microbov) names(temp) salers <- temp$Salers zebu <- temp$Zebu borgou <- temp$Borgou somba <- temp$Somba ## let's make some... Zeblers zebler <- hybridize(salers, zebu, n=40) ## and some Somgou somgou <- hybridize(somba, borgou, n=40) ## now let's merge all data into a single genind newDat <- repool(microbov, zebler, somgou) ## make a correspondance analysis ## and see where hybrids are placed if(require(ade4)){ X <- genind2genpop(newDat,missing="chi2",quiet=TRUE) coa1 <- dudi.coa(as.data.frame(X$tab),scannf=FALSE,nf=3) s.label(coa1$li,label=X$pop.names) add.scatter.eig(coa1$eig,2,1,2) }