dartR.base (version 1.0.5)

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

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Usage

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

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].

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].

Author

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

Details

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.

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.

See Also

Other utilities: gl.alf(), utils.collapse.matrix(), utils.dart2genlight(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.is.fixed(), utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose(), utils.vcfr2genlight.polyploid()

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')