paturley
commented
6 months ago I'm confused by your question. MTAG looks for a column that corresponds to the frequency of the effect allele. It looks like the column it has picked out is your MAF column. Do you prefer it to use a different column? You can force it to use the right column with the --eaf_name option.
Best, Patrick
On Sun, Apr 28, 2024 at 3:48 AM caiwenjie10 @.***> wrote:
Hello, I converted the allele frequencies from the reference panel to MAF and incorporated them, but it identified MAF as "Allele frequency." Is this correct? I would appreciate clarification. Thank you. 2024/04/16/07:55:50 PM Beginning MTAG analysis... 2024/04/16/07:55:50 PM MTAG will use the Z column for analyses. 2024/04/16/07:56:16 PM Read in Trait 1 summary statistics (17103079 SNPs) from /gpfsnew/lab/groupYU/members/liumengge/caiwenjie/mtag/223.temp2_with_maf.txt ... 2024/04/16/07:56:16 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2024/04/16/07:56:16 PM Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< 2024/04/16/07:56:16 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2024/04/16/07:56:16 PM Interpreting column names as follows: 2024/04/16/07:56:16 PM snpid: Variant ID (e.g., rs number) n: Sample size a1: a1, interpreted as ref allele for signed sumstat. pval: p-Value a2: a2, interpreted as non-ref allele for signed sumstat. MAF: Allele frequency z: Directional summary statistic as specified by --signed-sumstats.
2024/04/16/07:56:17 PM Reading sumstats from provided DataFrame into memory 10000000 SNPs at a time. 2024/04/16/07:56:42 PM Read 17103079 SNPs from --sumstats file.
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caiwenjie10
Hello, I converted the allele frequencies from the reference panel to MAF and incorporated them, but it identified MAF as "Allele frequency." Is this correct? I would appreciate clarification. Thank you. 2024/04/16/07:55:50 PM Beginning MTAG analysis... 2024/04/16/07:55:50 PM MTAG will use the Z column for analyses. 2024/04/16/07:56:16 PM Read in Trait 1 summary statistics (17103079 SNPs) from /gpfsnew/lab/groupYU/members/liumengge/caiwenjie/mtag/223.temp2_with_maf.txt ... 2024/04/16/07:56:16 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2024/04/16/07:56:16 PM Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< 2024/04/16/07:56:16 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2024/04/16/07:56:16 PM Interpreting column names as follows: 2024/04/16/07:56:16 PM snpid: Variant ID (e.g., rs number) n: Sample size a1: a1, interpreted as ref allele for signed sumstat. pval: p-Value a2: a2, interpreted as non-ref allele for signed sumstat. MAF: Allele frequency z: Directional summary statistic as specified by --signed-sumstats.
2024/04/16/07:56:17 PM Reading sumstats from provided DataFrame into memory 10000000 SNPs at a time. 2024/04/16/07:56:42 PM Read 17103079 SNPs from --sumstats file.