Accessors {polyRAD} | R Documentation |
Accessor Functions for RADdata Objects
Description
These functions can be used for accessing and replacing data within
a "RADdata"
object. Data slots that do not yet have
accessors can be accessed and replaced using the $
operator or the
attr
function.
Usage
GetTaxa(object, ...)
GetLoci(object, ...)
GetLocDepth(object, ...)
GetContamRate(object, ...)
SetContamRate(object, value, ...)
nTaxa(object, ...)
nLoci(object, ...)
nAlleles(object, ...)
GetAlleleNames(object, ...)
GetTaxaPloidy(object, ...)
SetTaxaPloidy(object, value, ...)
GetTaxaByPloidy(object, ...)
## S3 method for class 'RADdata'
GetTaxaByPloidy(object, ploidy, ...)
Arguments
object |
A |
value |
A value to assign. For |
ploidy |
An integer indicating a single ploidy for which to return taxa. |
... |
Additional arguments (none currently supported). |
Value
For GetTaxa
and GetLoci
, a character vector listing taxa names
or loci names, respectively. For GetLocDepth
, a named matrix with
taxa in rows and loci in columns, giving the total read depth for each taxon
and locus. For GetContamRate
, a number indicating the expected
contamination rate that is stored in the object. For SetContamRate
, a
"RADdata"
object with an updated contamination rate.
For nTaxa
, the number of taxa in the object. For nLoci
, the
number of loci in the object. For nAlleles
, the
number of alleles across all loci in the object. For GetAlleleNames
,
the names of all alleles. For GetTaxaPloidy
, a named integer vector
indicating the ploidy of each taxon. For SetTaxaPloidy
, a
"RADdata"
object with the taxa ploidies updated. For
GetTaxaByPloidy
, a character vector listing taxa.
Author(s)
Lindsay V. Clark
See Also
SetBlankTaxa
for functions that assign taxa to particular roles.
Examples
data(exampleRAD)
GetTaxa(exampleRAD)
GetLoci(exampleRAD)
GetLocDepth(exampleRAD)
GetContamRate(exampleRAD)
exampleRAD <- SetContamRate(exampleRAD, 0.0000001)
GetContamRate(exampleRAD)
nTaxa(exampleRAD)
nAlleles(exampleRAD)
GetAlleleNames(exampleRAD)
GetTaxaPloidy(exampleRAD)
exampleRAD <- SetTaxaPloidy(exampleRAD, rep(c(2, 5), time = c(75, 25)))
GetTaxaByPloidy(exampleRAD, 2)