「第一个问题：GWAS中0-1-2的编码？」. 应该都是采用这样的编码：主等位基因纯合编码为0，杂合为1，次等位基因纯合编码为2。 看一下plink的官网说明： --recode creates a new text fileset, after applying sample/variant filters and other operations.

Aug 5, 2014 · Treating it as 0/1/2 is essentially the dosage model, where you assuming have two of the minor alleles (homozygote minor) is twice the effect on the phenotype as having one of the minor alleles (heterozygote), and zero (homozygote major) is no effect.

Jul 15, 2020 · Genotype encodings {0, 1, 2} and {−1, 0, 1} correspond to measuring an additive effect at a SNP. Encoded genotype {0, 1, 2} represents the number of minor allele in the genotype and {−1, 0, 1} is associated with vanishing level of dominance.

Jun 16, 2015 · Making each nucleotides pair 0 or 2 is simple, but if there are other conditions then you either have to explain them or maybe try Biostars. While you could roll your own method to do this, I would suggest that for both the conversion and PCA that you use an …

May 1, 2019 · snpRecode is a function to convert SNP genotypes to 0, 1, and 2 for the homozygous, heterozygous, and other homozygous genotype, respectively.

This allows for the 0, 1, 2 count to reflect the number of a pre-specified allele type per SNP, rather than the number of the minor allele. This command takes as a single argument the name of a file that lists SNP name and allele to report, e.g. if the file recode.txt contained snp1 1 snp2 A then

converts 3406 SNP marker loci genotypic classes (0, 1, 2) to format required by GS3 (11, 12, 22). data A (drop=i); set pc.alleles ; array svars $ a1-a3406; array gvars $ g1-g3406; do i= 1 to 3406; if not missing (svars[i]) then do; if svars[i] ='0' then gvars[i]='11'; if svars[i] ='1' then gvars[i]='12'; if svars[i] ='2' then gvars[i]='22';

If you need to have a plain genoty (0,1 2), then you can assign randomly based on genotype frequencies. You might want to do it several times to see the sensitivity of your procedure to this imputation.

snpRecode is a function to convert SNP genotypes to 0, 1, and 2 for the homozygous, heterozygous, and other homozygous genotype, respectively.

ANSWER: The r package snpReady can convert matrices in nitrogenous base format to 0 1 2: https://cran.r-project.org/web/packages/snpReady/snpReady.pdf. Login before adding your answer.