adegenet: seploc – R documentation

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seploc

Separate data per locus

Description

The function seploc splits an object (genind, genpop or genlight) by marker. For genind and genpop objects, the method returns a list of objects whose components each correspond to a marker. For genlight objects, the methods returns blocks of SNPs.

Usage

## S4 method for signature 'genind'
seploc(x,truenames=TRUE,res.type=c("genind","matrix"))
## S4 method for signature 'genpop'
seploc(x,truenames=TRUE,res.type=c("genpop","matrix"))
## S4 method for signature 'genlight'
seploc(x, n.block=NULL, block.size=NULL, random=FALSE,
       parallel=FALSE, n.cores=NULL)

Arguments

`x`	a genind or a genpop object.
`truenames`	a logical indicating whether true names should be used (TRUE, default) instead of generic labels (FALSE).
`res.type`	a character indicating the type of returned results, a genind or genpop object (default) or a matrix of data corresponding to the 'tab' slot.
`n.block`	an integer indicating the number of blocks of SNPs to be returned.
`block.size`	an integer indicating the size (in number of SNPs) of the blocks to be returned.
`random`	should blocks be formed of contiguous SNPs, or should they be made or randomly chosen SNPs.
`parallel`	a logical indicating whether multiple cores -if available- should be used for the computations (TRUE, default), or not (FALSE); requires the package `parallel` to be installed.
`n.cores`	if `parallel` is TRUE, the number of cores to be used in the computations; if NULL, then the maximum number of cores available on the computer is used.

Value

The function seploc returns an list of objects of the same class as the initial object, or a list of matrices similar to x\$tab.

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

## Not run: 
## example on genind objects
data(microbov)

# separate all markers
obj <- seploc(microbov)
names(obj)

obj$INRA5


## example on genlight objects
x <- glSim(100, 1000, 0, ploidy=2) # simulate data
x <- x[,order(glSum(x))] # reorder loci by frequency of 2nd allele
glPlot(x, main="All data") # plot data
foo <- seploc(x, n.block=3) # form 3 blocks
foo
glPlot(foo[[1]], main="1st block") # plot 1st block
glPlot(foo[[2]], main="2nd block") # plot 2nd block
glPlot(foo[[3]], main="3rd block") # plot 3rd block

foo <- seploc(x, block.size=600, random=TRUE) # split data, randomize loci
foo # note the different block sizes
glPlot(foo[[1]])

## 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