The issue regarding the use of MAF.

[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.

[paturley]

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

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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. — Reply to this email directly, view it on GitHub <#210>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5ORPJIKPVMA32FCIWTY7SSWDAVCNFSM6AAAAABG4YWZVKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3DONBRGE3TSNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[caiwenjie10]

Dear Professor,
Thank you for your response, I have understood my own question now. Additionally, I would like to ask, which column is needed for MTAG analysis, the MAF column or the EAF column?Thank you.

[paturley]

Better to use the EAF column if it's available. Best, Patrick

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On Mon, Apr 29, 2024 at 8:44 PM CAIcaicai ***@***.***> wrote: Dear Professor, Thank you for your response, I have understood my own question now. Additionally, I would like to ask, for MTAG analysis, is it necessary to use the MAF column or the EAF column? Thank you. — Reply to this email directly, view it on GitHub <#210 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFBUB5POXAZZZ7KU67DMF7DY73SO7AVCNFSM6AAAAABG4YWZVKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTHE3TKNRQHA> . You are receiving this because you commented.Message ID: ***@***.***>

[caiwenjie10]

Thank you very much for your response!I am very grateful.