mtag
mtag copied to clipboard
JonJala
error occurred when estimating baseline maxFDR
Dear authors and users,
I ran maxFDR on each of the sets of summary statistics separately to estimate their corresponding basline maxFDR as suggested by paturley (https://github.com/omeed-maghzian/mtag/issues/61#issuecomment-460291600). It worked for some traits but for the others. Errors occurring during the estimation can be found in these two log files.
Any comments on the causes of these errors and how they can be fixed are highly appreciated.
Many thanks, xuemin gwas_sumstats_2.log.log gwas_sumstats_1.log.log
Apologies for the delays in responding to this and your other issues. I'm backlogged trying to meet a big deadline for next week. I'll respond to these as soon as possible.
Hi Paturley,
I encountered the same error as Xuemin reported above in "gwas_sumstats_1.log.log". The only difference was that the error occurred when I perform basic MTAG on two GWAS sumstats. The program reported "KeyError: 'CHR0'" after it completed the merge of GWAS summary statistics. So I also concern about your comments on the causes of this error and how it can be fixed.
Many thanks
It looks like you may need to do some data QC before passing your summary statistics into MTAG. For example, please verify that the ref and alt alleles are only A, T, C, or G and that the chromosome numbers are 1-22.
On Fri, Jun 5, 2020 at 1:40 AM zhwang [email protected] wrote:
Hi Paturley,
I encountered the same error as Xuemin reported above in "gwas_sumstats_1.log.log". The only difference was that the error occurred when I perform basic MTAG on two GWAS sumstats. The program reported "KeyError: 'CHR0'" after it completed the merge of GWAS summary statistics. So I also concern about your comments on the causes of this error and how it can be fixed.
Many thanks
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/omeed-maghzian/mtag/issues/96#issuecomment-639271047, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5NMZKLLAMAPSCS2DQDRVCAODANCNFSM4NNCBYMA .
Hi wzhnku,
I also met the same issue as you did. I tried to match the snpid, allele order, and also matched the HapMap3 before running MTAG. However, it still returned "KeyError: 'CHR0'".
Did you somehow manage to solve this issue?
Cheers, Angli
Hi Paturley,
I encountered the same error as Xuemin reported above in "gwas_sumstats_1.log.log". The only difference was that the error occurred when I perform basic MTAG on two GWAS sumstats. The program reported "KeyError: 'CHR0'" after it completed the merge of GWAS summary statistics. So I also concern about your comments on the causes of this error and how it can be fixed.
Many thanks
Hi wzhnku,
I also met the same issue as you did. I tried to match the snpid, allele order, and also matched the HapMap3 before running MTAG. However, it still returned "KeyError: 'CHR0'".
Did you somehow manage to solve this issue?
Cheers, Angli
Hi Paturley, I encountered the same error as Xuemin reported above in "gwas_sumstats_1.log.log". The only difference was that the error occurred when I perform basic MTAG on two GWAS sumstats. The program reported "KeyError: 'CHR0'" after it completed the merge of GWAS summary statistics. So I also concern about your comments on the causes of this error and how it can be fixed. Many thanks
Hi Angli,
After receiving Paturley's reply, I noticed that some columns required by MTAG were not listed in my original GWAS sumstats. After completing my data and "munging" them into the format required by MTAG, this issue solved.
So maybe you could check your sumstats data and make sure they have all the columns required by MTAG, i.e. snpid, chr, bpos, a1, a2, freq, z(beta/se), oval and n.
Best, Zihang
Hi wzhnku, I also met the same issue as you did. I tried to match the snpid, allele order, and also matched the HapMap3 before running MTAG. However, it still returned "KeyError: 'CHR0'". Did you somehow manage to solve this issue? Cheers, Angli
Hi Paturley, I encountered the same error as Xuemin reported above in "gwas_sumstats_1.log.log". The only difference was that the error occurred when I perform basic MTAG on two GWAS sumstats. The program reported "KeyError: 'CHR0'" after it completed the merge of GWAS summary statistics. So I also concern about your comments on the causes of this error and how it can be fixed. Many thanks
Hi Angli,
After receiving Paturley's reply, I noticed that some columns required by MTAG were not listed in my original GWAS sumstats. After completing my data and "munging" them into the format required by MTAG, this issue solved.
So maybe you could check your sumstats data and make sure they have all the columns required by MTAG, i.e. snpid, chr, bpos, a1, a2, freq, z(beta/se), oval and n.
Best, Zihang
Hi Zihang,
Thanks for your suggestions. After I matched all the required columns, it ran well as I expected.
Cheers, Angli