SubsetByTaxon: Create RADdata Object with a Subset of Taxa

In polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Create RADdata Object with a Subset of Taxa

Description

This function is used for removing some of the taxa from a dataset stored in a RADdata object.

Usage

SubsetByTaxon(object, ...)
## S3 method for class 'RADdata'
SubsetByTaxon(object, taxa, ...)

Arguments

object	A RADdata object.
taxa	A character or numeric vector indicating which taxa to retain in the output.
...	Additional arguments (none implemented).

Details

This function may be used for subsetting a RADdata object either immediately after data import, or after additional analysis has been performed. Note however that estimation of allele frequencies, genotype prior probabilities, PCA, etc. are very dependent on what samples are included in the dataset. If those calculations have already been performed, the results will be transferred to the new object but not recalculated.

Value

A RADdata object containing only the taxa listed in taxa.

Author(s)

Lindsay V. Clark

See Also

SubsetByLocus

Examples

# load data for this example
data(exampleRAD)
exampleRAD

# just keep the first fifty taxa
subsetRAD <- SubsetByTaxon(exampleRAD, 1:50)
subsetRAD

polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.