SetBlankTaxa {polyRAD} | R Documentation |
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 |
value |
A character string (or a character vector for |
... |
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)