Remove all but specified populations from a genelight {adegenet} object
Individuals are assigned to populations based on the specimen metadata data file (csv) used with gl.read.dart().
gl.keep.pop( x, pop.list, as.pop = NULL, recalc = FALSE, mono.rm = FALSE, verbose = NULL )
x |
– name of the genlight object containing SNP genotypes or a genind object containing presence/absence data [required] |
pop.list |
– a list of populations to be kept [required] |
as.pop |
– assign another metric to represent population [default NULL] |
recalc |
– Recalculate the locus metadata statistics [default FALSE] |
mono.rm |
– Remove monomorphic loci [default FALSE] |
verbose |
– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity] |
The script, having deleted the specified populations, optionally identifies resultant monomorphic loci or loci with all values missing and deletes them (using gl.filter.monomorphs.r). The script also optionally recalculates statistics made redundant by the deletion of individuals from the dataset.
The script returns a genlight object with the new population assignments and the recalculated locus metadata.
A genlight object with the reduced data
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
gl.filter.monomorphs for when mono.rm=TRUE, gl.recalc.metrics for when recalc=TRUE
gl.drop.pop to drop rather than keep specified populations
# SNP data
gl2 <- gl.keep.pop(testset.gl, pop.list=c("EmsubRopeMata","EmvicVictJasp"))
gl2 <- gl.keep.pop(testset.gl, pop.list=c("EmsubRopeMata","EmvicVictJasp"),
mono.rm=TRUE,recalc=TRUE)
gl2 <- gl.keep.pop(testset.gl, pop.list=c("Female"),as.pop="sex")
# Tag P/A data
gs2 <- gl.keep.pop(testset.gs, pop.list=c("EmsubRopeMata","EmvicVictJasp"))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.