error
fry3682665 opened this issue · 8 comments
This is indeed weird! Are you just testing the example files? I will look into it.
It is not a test file, but my own GWAS Summary file, because in my previous use it seems that the HDL operation can only be performed if I change my file name to the same file name as the test file and remove the test file.
This is my data. Is there a problem with the data?Another request is that I am also having trouble with this data when doing LDSC analysis. The problem has been commented on the GIthub of LDSC and I really hope to get your advice
It is not a test file, but my own GWAS Summary file, because in my previous use it seems that the HDL operation can only be performed if I change my file name to the same file name as the test file and remove the test file.
HDL should be smarter :) You should be able to specify your own file name by setting gwas1.df= and gwas1.df=.
This is my data. Is there a problem with the data?Another request is that I am also having trouble with this data when doing LDSC analysis. The problem has been commented on the GIthub of LDSC and I really hope to get your advice
The only thing I find a bit abnormal according to the screenshot is that most of SNPs are without rsid. How many SNPs you have in the GWAS files? Could you try to run with UKB_imputed_SVD_eigen99_extraction reference panel? This is the most standard panel we recommend our users to use. This panel is a subset of LDSC 1000 Genomes panel. If too many SNPs in this panel miss in your GWAS, then there might be some issue for both HDL and LDSC.
Thank you very much. It seems that the lack of SNPID is my main mistake. I still want to ask you how to add SNPID in GWAS Summary
It is not a test file, but my own GWAS Summary file, because in my previous use it seems that the HDL operation can only be performed if I change my file name to the same file name as the test file and remove the test file.
HDL should be smarter :) You should be able to specify your own file name by setting
gwas1.df=andgwas1.df=.
This is my data. Is there a problem with the data?Another request is that I am also having trouble with this data when doing LDSC analysis. The problem has been commented on the GIthub of LDSC and I really hope to get your adviceThe only thing I find a bit abnormal according to the screenshot is that most of SNPs are without rsid. How many SNPs you have in the GWAS files? Could you try to run with UKB_imputed_SVD_eigen99_extraction reference panel? This is the most standard panel we recommend our users to use. This panel is a subset of LDSC 1000 Genomes panel. If too many SNPs in this panel miss in your GWAS, then there might be some issue for both HDL and LDSC.
I used my own file name, the data format conversion was complete, and the HDL operation didn't work at all
I am eager to get your help
It is not a test file, but my own GWAS Summary file, because in my previous use it seems that the HDL operation can only be performed if I change my file name to the same file name as the test file and remove the test file.
HDL should be smarter :) You should be able to specify your own file name by setting
gwas1.df=andgwas1.df=.
This is my data. Is there a problem with the data?Another request is that I am also having trouble with this data when doing LDSC analysis. The problem has been commented on the GIthub of LDSC and I really hope to get your adviceThe only thing I find a bit abnormal according to the screenshot is that most of SNPs are without rsid. How many SNPs you have in the GWAS files? Could you try to run with UKB_imputed_SVD_eigen99_extraction reference panel? This is the most standard panel we recommend our users to use. This panel is a subset of LDSC 1000 Genomes panel. If too many SNPs in this panel miss in your GWAS, then there might be some issue for both HDL and LDSC.
I used my own file name, the data format conversion was complete, and the HDL operation didn't work at all
I am eager to get your help
The names of arguments for HDL should be: 'gwas1.df' and 'gwas2.df', instead of 'asd.df' and 'ra.df'. You can change them and try it again.