gl.sort: Sorts genlight objects

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Sorts genlight objects

Description

This function provides the ability to sort genotypes in a genlight object by individual name or population name.

Usage

gl.sort(x, sort.by = "pop", order.by = NULL, verbose = NULL)

Arguments

x	Genlight object containing SNP/Silicodart genotypes [required].
sort.by	Specify to sort the genotypes by either 'ind', "pop" [default 'pop'].
order.by	Vector used to order genotypes [default NULL]
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity]

Details

This is a function to sort genotypes in a genlight object by individual name or population name. This will be useful if you want to visualise the structure across populations (bands) in a gl.smearplot; order of genotypes is important.

The order.by parameter needs to be a vector upon which to effect the sort, of length of nPop(gl) if sort.by is 'pop' or nInd(gl) if sort.by is 'ind'. For sort.by='ind' order.by can be a vector such as a variable in gl@other$ind.metrics.

If not specified by nominating a vector with order.by, alphabetical order of populations or individuals is used.

Value

Returns a reordered genlight object. Sorts also the ind/loc.metrics and coordinates accordingly

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

See Also

Other data manipulation: gl.define.pop(), gl.drop.ind(), gl.drop.loc(), gl.drop.pop(), gl.edit.recode.pop(), gl.impute(), gl.join(), gl.keep.ind(), gl.keep.loc(), gl.keep.pop(), gl.make.recode.ind(), gl.merge.pop(), gl.reassign.pop(), gl.recode.ind(), gl.recode.pop(), gl.rename.pop(), gl.sample(), gl.sim.genotypes(), gl.subsample.ind(), gl.subsample.loc()

Examples

#sort by populations
bc <- gl.sort(bandicoot.gl)
#sort from West to East
bc2 <- gl.sort(bandicoot.gl, sort.by="pop" ,
order.by=c("WA", "SA", "VIC", "NSW", "QLD"))
#sort by missing values
miss <- rowSums(is.na(as.matrix(bandicoot.gl)))
bc3 <- gl.sort(bandicoot.gl, sort.by="ind", order.by=miss)
gl.smearplot(bc3)

dartR.base documentation built on April 4, 2025, 2:45 a.m.