Please make sure that this is a bug! If you have questions about how to use TwoSampleMR please use the Discussions function instead.
Describe the bug (required)
I have about 100 SNPs for 28 genes to clump. After "clump_data", 1 of the 28 genes "SERPINA7" is removed. Because the error contains "Removing 2 of 2 variants due to LD with other variants or absence from LD reference panel", to make things simple, I created a file with the only 2 SNPs for SERPINA7 as follows:
SNP beta se effect_allele other_allele Phenotype chr pval NOTE id
rs1804495 -0.112 0.0157727796563968 T G SERPINA7 X 1.24e-12 use beta as beta directly from the local file Mydataset.SERPINA7
rs5916968 -0.112 0.0158231494269504 A G SERPINA7 X 1.46e-12 use beta as beta directly from the local file Mydataset.SERPINA7
Then "format_data", and then "clump_data".
The weird thing is that it always generate the following errors:
Clumping Mydataset.SERPINA7, 2 variants, using EUR population reference
Server code: 503; Server is possibly experiencing traffic, trying again...
Server code: 503; Server is possibly experiencing traffic, trying again...
Server code: 503; Server is possibly experiencing traffic, trying again...
Server code: 503; Server is possibly experiencing traffic, trying again...
fdatServer code: 503; Server is possibly experiencing traffic, trying again...
Server code: 503; Server is possibly experiencing traffic, trying again...
Server error: 503
Failed to retrieve results from server. See error status message in the returned object and contact the developers if the problem persists.
Removing 2 of 2 variants due to LD with other variants or absence from LD reference panel
Please note the Server error. I don't think this is due to the server being down, because 1) the same thing happened a week ago; 2) it only happens to the 2 SERPINA7 SNPs, other SNPs and genes are OK (i.e. no "Server error" and at least 1 SNP is kept for every gene); 3) it tried it several times for SERPINA7 & other genes (separately or together) today and all other genes are always OK, and the SERPINA7 gene is not.
So my question is: why is SERPINA7 so special? The p-value is OK, the eaf is missing but should not be the problem (SNPs for other genes do not have eaf, either; I filled in the eaf for the 2 SNPs and that didn't help).
The only thing that I can think of is that SERPINA7 is on chrX. In the data file above, I used "X" for the chr. I also tried "23" for chrX and the results are the same -- server error and all the 2 snps are removed after clumping.
Provide a clear and concise description of what the bug is
See above
Describe the current behaviour you observe (required)
See above
Include code blocks with any error messages
See above
Please make sure that this is a bug! If you have questions about how to use TwoSampleMR please use the Discussions function instead.
Describe the bug (required)
I have about 100 SNPs for 28 genes to clump. After "clump_data", 1 of the 28 genes "SERPINA7" is removed. Because the error contains "Removing 2 of 2 variants due to LD with other variants or absence from LD reference panel", to make things simple, I created a file with the only 2 SNPs for SERPINA7 as follows:
Then "format_data", and then "clump_data".
The weird thing is that it always generate the following errors:
Please note the Server error. I don't think this is due to the server being down, because 1) the same thing happened a week ago; 2) it only happens to the 2 SERPINA7 SNPs, other SNPs and genes are OK (i.e. no "Server error" and at least 1 SNP is kept for every gene); 3) it tried it several times for SERPINA7 & other genes (separately or together) today and all other genes are always OK, and the SERPINA7 gene is not.
So my question is: why is SERPINA7 so special? The p-value is OK, the eaf is missing but should not be the problem (SNPs for other genes do not have eaf, either; I filled in the eaf for the 2 SNPs and that didn't help).
The only thing that I can think of is that SERPINA7 is on chrX. In the data file above, I used "X" for the chr. I also tried "23" for chrX and the results are the same -- server error and all the 2 snps are removed after clumping.
Provide a clear and concise description of what the bug is See above
Describe the current behaviour you observe (required)
See above
Include code blocks with any error messages See above
Describe the behaviour you expect (required)
See above
R code to reproduce the issue (required)
Please provide a minimal code snippet that will reproduce this issue see the R code above
Contribute a solution (optional)
Please submit a pull request and/or briefly describe your proposed solution
System information
Please provide details of your operating system and R version I am using ubuntu: 5.15.0-46-generic #49-Ubuntu SMP R: R version 4.1.2 (2021-11-01)
Additional context
Add any other context about the problem here