GetTaxa: Accessor Functions for RADdata Objects

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

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 "RADdata" object.
value	A value to assign. For SetContamRate, a number generally ranging from zero to 0.01 indicating the expected rate of sample cross-contamination. For SetTaxaPloidy, a vector of integers indicating ploidy, with one value for each taxon. If the vector for SetTaxaPloidy is named, the names should correspond to taxa names in the object.
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)

lvclark/polyRAD documentation built on Jan. 15, 2024, 4:19 a.m.