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1
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I am curious about the relationship between your p-value (or effect sizes) and standard error. I would expect the significant signals to have smaller stand error compared to the non-significant, backg …
answered May 12 '20 by Phoenix Mu
1
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as mentioned in previous answers, transformations are frequently used. One commonly used method is quantile normal transformation. Basically you calculate the quantile from the original data and match …
answered Feb 15 '21 by Phoenix Mu
2
votes
You can use --pheno to specify a phenotype file you want to use, the 1st and 2nd columns being FID and IID. These are just used on the fly and cannot be written to the BED files as I understand. --mak …
answered Feb 18 '21 by Phoenix Mu
3
votes
As for why running GWAS using single SNP. In a GWAS, it is typical to use 500K to 7M SNPs. So this is a large number. … Now since we are running GWAS in an SNP-by-SNP fashion, there are a lot of work that needs to be done after GWAS in order to find the true causal SNP. …
answered Mar 26 '20 by Phoenix Mu
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The first way is to combine two samples and re-run GWAS. A second way is to do a meta-analysis using GWAS results. …
answered May 5 '20 by Phoenix Mu