Hi, everyone.
I had read a paper titled "Multiple Instances of Ancient balancing selection shared between humans and chimpanzees". In the paper, there are 59 human individuals (36 females and 23 males) and 10 chimpanzee (9 females and 1 male). After snps were phased, significant LD were defined as follow: "In humans, we used the phased data provided by paper-1 and applied a Chi-square test, considering a p-value less than 0.005 as significant (i.e., r2 > 0.065) (35). For SNPs lacking phase information, we used the genotype data to calculate r2 and took the same cutoff for significance (r2 > 0.065). In chimpanzees, where the sample size is smaller, we applied Fisher’s exact test to the phased data obtained in paper-2 and regarded a p-value less than 0.1 as significant. For the unphased SNPs on the X chromosome, we applied a Chi-square test to the genotype data, considering a p-value less than 0.1 as significant (i.e., r2 > 0.135). "
I don't know how the threshold were calculated. I had found a formula by google, Chi-square=N*(r-square), and Chi-square(0.05, df-1)=3.84, since there are 59 individuals, so 3.85/59=0.065, am I right? And what about Fisher's exact test and how it was calculated? And how about X chromosome, since it only have one in male, if using above formula in Chi-square, what is N? Also, whether X chromosome in human and chimpanzee all use Chi-square with p-value less than 0.1 or human use Chi-square while chimpanzee still using Fisher's exact test?
Thanks for any suggestion!
Best wishes!
I had read a paper titled "Multiple Instances of Ancient balancing selection shared between humans and chimpanzees". In the paper, there are 59 human individuals (36 females and 23 males) and 10 chimpanzee (9 females and 1 male). After snps were phased, significant LD were defined as follow: "In humans, we used the phased data provided by paper-1 and applied a Chi-square test, considering a p-value less than 0.005 as significant (i.e., r2 > 0.065) (35). For SNPs lacking phase information, we used the genotype data to calculate r2 and took the same cutoff for significance (r2 > 0.065). In chimpanzees, where the sample size is smaller, we applied Fisher’s exact test to the phased data obtained in paper-2 and regarded a p-value less than 0.1 as significant. For the unphased SNPs on the X chromosome, we applied a Chi-square test to the genotype data, considering a p-value less than 0.1 as significant (i.e., r2 > 0.135). "
I don't know how the threshold were calculated. I had found a formula by google, Chi-square=N*(r-square), and Chi-square(0.05, df-1)=3.84, since there are 59 individuals, so 3.85/59=0.065, am I right? And what about Fisher's exact test and how it was calculated? And how about X chromosome, since it only have one in male, if using above formula in Chi-square, what is N? Also, whether X chromosome in human and chimpanzee all use Chi-square with p-value less than 0.1 or human use Chi-square while chimpanzee still using Fisher's exact test?
Thanks for any suggestion!
Best wishes!