SetBlankTaxa: Functions to Assign Taxa to Specific Roles

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

Functions to Assign Taxa to Specific Roles

Description

These functions are used for assigning and retrieving taxa from a "RADdata" object that serve particular roles in the dataset. Blank taxa can be used for estimating the contamination rate (see EstimateContaminationRate), and the donor and recurrent parents are used for determining expected genotype distributions in mapping populations. Many functions in polyRAD will automatically exclude taxa from analysis if they have been assigned to one of these roles.

Usage

SetBlankTaxa(object, value)
GetBlankTaxa(object, ...)
SetDonorParent(object, value)
GetDonorParent(object, ...)
SetRecurrentParent(object, value)
GetRecurrentParent(object, ...)

Arguments

object	A "RADdata" object.
value	A character string (or a character vector for SetBlankTaxa) indicating the taxon or taxa to be assigned to the role.
...	Other arguments (none currently supported).

Value

For the “Get” functions, a character vector indicating the taxon or taxa that have been assigned to that role. For the “Set” functions, a "RADdata" object identical to the one passed to the function, but with new taxa assigned to that role.

Author(s)

Lindsay V. Clark

See Also

AddGenotypePriorProb_Mapping2Parents

Examples

# assign parents in a mapping population
data(exampleRAD_mapping)
exampleRAD_mapping <- SetDonorParent(exampleRAD_mapping, "parent1")
exampleRAD_mapping <- SetRecurrentParent(exampleRAD_mapping, "parent2")
GetDonorParent(exampleRAD_mapping)
GetRecurrentParent(exampleRAD_mapping)

# assign blanks
exampleRAD_mapping <- SetBlankTaxa(exampleRAD_mapping, 
                                   c("progeny019", "progeny035"))
GetBlankTaxa(exampleRAD_mapping)

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