| gl.drop.ind {dartR.base} | R Documentation |
Removes specified individuals from a dartR genlight object
Description
This function deletes individuals and their associated metadata. Monomorphic loci and loci that are scored all NA are optionally deleted (mono.rm=TRUE). The script also optionally recalculates locus metatdata statistics to accommodate the deletion of individuals from the dataset (recalc=TRUE).
The script returns a dartR genlight object with the retained individuals and the recalculated locus metadata. The script works with both genlight objects containing SNP genotypes and Tag P/A data (SilicoDArT).
Usage
gl.drop.ind(x, ind.list, recalc = FALSE, mono.rm = FALSE, verbose = NULL)
Arguments
x |
Name of the genlight object [required]. |
ind.list |
List of individuals to be removed [required]. |
recalc |
If TRUE, recalculate the locus metadata statistics [default FALSE]. |
mono.rm |
If TRUE, remove monomorphic and all NA loci [default FALSE]. |
verbose |
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress but not results; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]. |
Value
A reduced dartR genlight object
Author(s)
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
See Also
gl.keep.ind to keep rather than drop specified
individuals
Other data manipulation:
gl.define.pop(),
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.sort(),
gl.subsample.ind(),
gl.subsample.loc()
Examples
# SNP data
gl2 <- gl.drop.ind(testset.gl,
ind.list=c('AA019073','AA004859'))
# Tag P/A data
gs2 <- gl.drop.ind(testset.gs,
ind.list=c('AA020656','AA19077','AA004859'))
gs2 <- gl.drop.ind(testset.gs, ind.list=c('AA020656'
,'AA19077','AA004859'),mono.rm=TRUE, recalc=TRUE)