utils.vcfr2genlight.polyploid: Utility function to convert polyploid vcfR object as genlight

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Utility function to convert polyploid vcfR object as genlight

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.vcfr2genlight.polyploid(x, n.cores = 1, mode2 = mode)

Arguments

x	Name of the vcfR object [defined in function gl.read.vcf].
n.cores	Number of cores [default 1]
mode2	genotype: all heterozygous sites will be coded as 1 regardless ploidy level, dosage: sites will be codes as copy number of alternate allele [defined in function gl.read.vcf].

Details

This function uses parameters from gl.read.vcf for conversion Note also that this function checks to see if there are input of mode, missing input of mode will issued the user with a error. "Dosage" mode of this function assign ploidy levels as maximum copy number of alternate alleles. Please carefully check the data if "dosage" mode is used. (codes were modified from 'vcfR2genlight' in vcfR packge to convert polyploid data)

Value

genlight object

Author(s)

Custodian: Ching Ching Lau – Post to https://groups.google.com/d/forum/dartr

References

• Knaus, B. J., & Grunwald, N. J. (2017). vcfr: a package to manipulate and visualize variant call format data in R. Molecular ecology resources, 17(1), 44-53.

• Knaus, B. J., Grunwald, N. J., Anderson, E. C., Winter, D. J., Kamvar, Z. N., & Tabima, J. F. (2023). Package 'vcfR'. vcfR

See Also

Other utilities: gl.alf(), utils.check.datatype(), 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()

Examples

## Not run: 
datatype <- utils.vcfr2genlight.polyploid(x=vcfr, mode2="genotype")

## End(Not run)

dartR.base documentation built on April 4, 2025, 2:45 a.m.