What does 0,1 and 2 exactly represent in additive coding?
Dear Kridsadakorn,
I would like to compute pairwise Hudson's Fst using your package KRIS, using the fst.each.snp.hudson(X, idx.p1, idx.p2) function. You mention that X represents "a matrix that contains the number 0, 1, and 2 representing SNP in additive coding. Rows represent individuals and columns represent SNP". I have some questions:
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By additive you mean 0,1 or 2 minor alleles per individual, even if the minor allele is not the same in the two populations?, or does the minor allele identity need to be matched in the 2 populations before getting 0,1 and 2 ?
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Can I get X by simply loading the .raw file created with the Plink --additive A flag, skipping the first 6 columns?:
plink --file data --recode A
http://zzz.bwh.harvard.edu/plink/dataman.shtml
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If 2 is false, do you know any function/tool suitable for generating X from Plink files?
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I am not sure how to visualise in R the "example_SNP" file loaded in the corresponding example. Do you have any suggestion?
Thank you very much in advance
All the best