Error when using format_data

[xuj18]

Dear Dr. Yang,

Sorry that I have another question regarding the format_data function in MR APSS.

When I was trying to run the script based on your tutorial, I got the error message as following:

AN_QC1 <- format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", ncontrol_col = "Nco", info_col = "INFO", A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P")

Error in format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", :
unused arguments (A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P")

I don't know why the A1_col, A2_col, b_col, freq_col and p_col are not recognized by the format_data function. I also double checked my summary statistic file to make sure the column names I specified here are all correct.

Any help would be appreciated. Thank you!

Best,
Jiayi

[hxh0928]

Dear Jiayi, I think you can try: AN_QC1 <- format_data(dat = AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", ncontrol_col = "Nco", info_col = "INFO", A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") by adding “dat = “ before AN-raw This is because the function has other default settings like "snps.merge = w_hm3.snplist”,"snps.remove = MHC.SNPs” , before snp_col = “SNP”. If we do not specify “dat = “ , the function may fail to identify these arguments. I will find a way to refine this. Thank you Bests, Xianghong 2024年9月14日 上午3:47，Jiayi_Xu ***@***.***> 写道： Dear Dr. Yang, Sorry that I have another question regarding the format_data function in MR APSS. When I was trying to run the script based on your tutorial, I got the error message as following: AN_QC1 <- format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", ncontrol_col = "Nco", info_col = "INFO", A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") Error in format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", : unused arguments (A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") I don't know why the A1_col, A2_col, b_col, freq_col and p_col are not recognized by the format_data function. I also double checked my summary statistic file to make sure the column names I specified here are all correct. Any help would be appreciated. Thank you! Best, Jiayi — Reply to this email directly, view it on GitHub<#5>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAZWMYNGGB44R4QF62EOIXDZWM6LRAVCNFSM6AAAAABOF7T36WVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDKNJWGM2DMNI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[xuj18]

Dear Xianghong, Thanks for your note back! I’ll give it a try and let you know if there is any further question. Thank you! Best, Jiayi From: hxh0928 ***@***.***> Date: Thursday, September 19, 2024 at 2:37 AM To: YangLabHKUST/MR-APSS ***@***.***> Cc: Xu, Jiayi ***@***.***>, Author ***@***.***> Subject: Re: [YangLabHKUST/MR-APSS] Error when using format_data (Issue #5) Dear Jiayi, I think you can try: AN_QC1 <- format_data(dat = AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", ncontrol_col = "Nco", info_col = "INFO", A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") by adding “dat = “ before AN-raw This is because the function has other default settings like "snps.merge = w_hm3.snplist”,"snps.remove = MHC.SNPs” , before snp_col = “SNP”. If we do not specify “dat = “ , the function may fail to identify these arguments. I will find a way to refine this. Thank you Bests, Xianghong 2024年9月14日 上午3:47，Jiayi_Xu ***@***.***> 写道： Dear Dr. Yang, Sorry that I have another question regarding the format_data function in MR APSS. When I was trying to run the script based on your tutorial, I got the error message as following: AN_QC1 <- format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", ncontrol_col = "Nco", info_col = "INFO", A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") Error in format_data(AN_raw, snp_col = "SNP", se_col = "SE", ncase_col = "Nca", : unused arguments (A1_col = "A1", A2_col = "A2", b_col = "beta", freq_col = "FRQ_U_1243971", p_col = "P") I don't know why the A1_col, A2_col, b_col, freq_col and p_col are not recognized by the format_data function. I also double checked my summary statistic file to make sure the column names I specified here are all correct. Any help would be appreciated. Thank you! Best, Jiayi — Reply to this email directly, view it on GitHub<#5>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAZWMYNGGB44R4QF62EOIXDZWM6LRAVCNFSM6AAAAABOF7T36WVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDKNJWGM2DMNI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APRMFSY2XVDXA3FYFPBV2CTZXJWI3AVCNFSM6AAAAABOF7T36WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRQGEYTAOJUHE>. You are receiving this because you authored the thread.Message ID: ***@***.***>