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.
utils.vcfr2genlight.polyploid(x, n.cores = 1, mode2 = mode)genlight object
Name of the vcfR object [defined in function gl.read.vcf].
Number of cores [default 1]
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].
Custodian: Ching Ching Lau -- Post to https://groups.google.com/d/forum/dartr
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)
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
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()
if (FALSE) {
datatype <- utils.vcfr2genlight.polyploid(x=vcfr, mode2="genotype")
}
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