utils.check.datatype: Utility function to check the class of an object passed to a...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Utility function to check the class of an object passed to a function

Description

Most functions require access to a genlight object, dist matrix, data matrix or fixed difference list (fd), and this function checks that a genlight object or one of the above has been passed, whether the genlight object is a SNP dataset or a SilicoDArT object, and reports back if verbosity is >=2.

Usage

utils.check.datatype(
  x,
  accept = c("genlight", "SNP", "SilicoDArT"),
  verbose = NULL
)

Arguments

x	Name of the genlight object, dist matrix, data matrix, glPCA, or fixed difference list (fd) [required].
accept	Vector containing the classes of objects that are to be accepted [default c('genlight','SNP','SilicoDArT'].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity].

Details

This function checks the class of passed object and sets the datatype to 'SNP', 'SilicoDArT', 'dist', 'mat', or class[1](x) as appropriate.

Note also that this function checks to see if there are individuals or loci scored as all missing (NA) and if so, issues the user with a warning.

Note: One and only one of gl.check, fd.check, dist.check or mat.check can be TRUE.

Value

datatype, 'SNP' for SNP data, 'SilicoDArT' for P/A data, 'dist' for a distance matrix, 'mat' for a data matrix, 'glPCA' for an ordination file, or class(x)[1].

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

 
datatype <- utils.check.datatype(testset.gl)
datatype <- utils.check.datatype(as.matrix(testset.gl),accept='matrix')
fd <- gl.fixed.diff(testset.gl)
datatype <- utils.check.datatype(fd,accept='fd')

datatype <- utils.check.datatype(testset.gl)

dartR documentation built on June 8, 2023, 6:48 a.m.