gl.sort: re-sorts genlight objects

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

re-sorts genlight objects

Description

Often it is desirable to have the genlight object sorted individuals by population names, indiviual name, for example to have a more informative gl.smearplot (showing banding patterns for populations). Also sorting by loci can be informative in some instances. This function provides the ability to sort individuals of a genlight object by providing the order of individuals or populations and also by loci metric providing the order of locis. See examples below for specifics.

Usage

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

Arguments

x	genlight object containing SNP/silicodart genotypes
sort.by	either "ind", "pop". Default is pop
order.by	that is used to order individuals or loci. Depening on the order.by parameter, this needs to be a vector of length of nPop(genlight) for populations or nInd(genlight) for individuals. If not specified alphabetical order of populations or individuals is used. For sort.by="ind" order.by can be also a vector specifying the order for each individual (for example another ind.metrics)
verbose	set verbosity

Details

This is convenience function to facilitate sorting of individuals within the genlight object. For example if you want to visualise the "band" of population in a gl.smearplot then the order of individuals is important. Also

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 base dartR: gl.sample()

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 documentation built on June 8, 2023, 6:48 a.m.