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Update README.md
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YangLabHKUST authored Aug 8, 2022
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Expand Up @@ -90,7 +90,7 @@ Next, an important step is to format the GWAS summary statistics for the MR_APSS
(7). remove SNPs with <img src="https://render.githubusercontent.com/render/math?math=\chi^2"> > <img src="https://render.githubusercontent.com/render/math?math=\chi^2_{max}">. The default value for <img src="https://render.githubusercontent.com/render/math?math=\chi^2_{max}"> is max(N/1000, 80).
allele frequency in case group and control group

**Q**: Does the allele frequency is required for MR-APSS to format GWAS summary statistics? What if I have columns of allele frequency in the case group ("freq_cases") and allele frequency in the control group ("freq_controls")?
**Q**: Does the allele frequency is required for MR-APSS to format GWAS summary statistics? What if I have columns of allele frequency in the case group ("freq_cases") and allele frequency in the control group ("freq_controls")?
**A**: Allele frequency ("freq_col"), as well as imputed information ("info_col"), are not required columns in GWAS summary statistics for MR-APSS to obtain the columns in the formatted datasets. To ensure the quality of SNPs, MR-APSS tries to exclude SNPs with MAF < 0.05. If allele frequencies are available in summary statistics, MR-APSS will remove SNPs with sample MAF < 0.05. Considering that sample MAF or imputed information may be missing from the GWAS summary statistics, like LDSC, MR-APSS restricts the analysis to a set of common and well-imputed SNPs in the HapMap 3 reference panel. If both "freq_cases" and "freq_controls" are available, one can obtain an estimation of MAF using the sample MAF of the control group. In MR-APSS, one can specify freq_col = “freq_controls”, or ignore "freq_col" when formatting data.

**Q**: What sample size do I need for MR-APSS?
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