seploc | R Documentation |
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.
## 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)
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 |
n.cores |
if |
The function seploc
returns an list of objects of the
same class as the initial object, or a list of matrices similar to
x$tab.
Thibaut Jombart t.jombart@imperial.ac.uk
seppop
, repool
## Not run: ## example on genind objects data(microbov) # separate all markers obj <- seploc(microbov) names(obj) obj$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)
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