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<div>Hi All adegenet guru,</div>
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<div>I am having troubles getting <i>df2genind</i> function to find the correct number of alleles in my dataset.</div>
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<div>My data are SNPs data (2 alleles at each locus). The genotypes are encoded in one single column such as 0=reference homozygote, 1=SNP homozygote and 2=heterozygote. And I importe them as data frame from a comma separated .csv file.</div>
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<div>When I apply the function df2genind,</div>
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<div>genind <- df2genind(locus, sep=",", ncode=1, NA.char="NA", ploidy=2)</div>
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<div>the genind object returned is as follow:</div>
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<div>/// GENIND OBJECT /////////</div>
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<div> // 1 individual; 2,078 loci; 5,752 alleles; size: 1.2 Mb</div>
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<div> // Basic content</div>
<div> @tab: 1 x 5752 matrix of allele counts</div>
<div> @loc.n.all: number of alleles per locus (range: 2-3)</div>
<div> @loc.fac: locus factor for the 5752 columns of @tab</div>
<div> @all.names: list of allele names for each locus</div>
<div> @ploidy: ploidy of each individual (range: 2-2)</div>
<div> @type: codom</div>
<div> @call: .local(x = x, i = i, j = j, drop = drop)</div>
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<div> // Optional content</div>
<div> - empty -</div>
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<div>There should be only 4,158 alleles in the object and not 5,752. Is there a problem with using this type of 0,1,2 code for the genotypes? Should my input have 2 columns for each genotype ?</div>
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<div>Thanks for your support!</div>
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<div>Cheers, Laura</div>
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