testing association between snp and the label disease

Question

[Eliza]

Hi, I'm trying to perform Cochran–Armitage test with SNPs in r. my data looks like this:

i found the cat function in R to perform that : catt(y, x, score = c(0, 1, 2)) I'm having trouble understanding how to encode the genotypes :

Y is the phenotype and X is supposed to be one column REF or ALT would apricient the help, have been stuck for hours. thank you

[iraun]

Hi @Eliza, this question is highly similar to your previous one at Cochran–Armitage test. To maintain the forum as informative as possible, if anything was not clear in the prior post or needs further explanation, it is best to add a comment there rather than posting a "new" question.