polyRAD (version 1.1)

Accessors: 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, ...)

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.

…

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.

See Also

SetBlankTaxa for functions that assign taxa to particular roles.

Examples

# NOT RUN {
data(exampleRAD)
GetTaxa(exampleRAD)
GetLoci(exampleRAD)
GetLocDepth(exampleRAD)
GetContamRate(exampleRAD)
exampleRAD <- SetContamRate(exampleRAD, 0.0000001)
GetContamRate(exampleRAD)
nTaxa(exampleRAD)
nAlleles(exampleRAD)
GetAlleleNames(exampleRAD)
# }