hxh0928
commented
1 month ago 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
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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