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qlu-lab / X-Wing

Cross-population weighting framework to improve genetic risk prediction in ancestrally diverse populations
GNU General Public License v3.0
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Error in checkForRemoteErrors(val): #1

Open LeqiXu opened 1 year ago

LeqiXu commented 1 year ago

After summary statistics of BMI being restricted to hm3 SNPs with LDHub filtering procedure, LOGODetect will produce error as showed in the figure. And I'd really appreciate it if you have any suggestions for that. LOGODetect_error

ghm17 commented 1 year ago

We have just updated the script LOGODetect.R. Please try the updated version and let us know if you still have errors.

xinyu-c9 commented 1 year ago

I still have the same error when I try the latest version of LOGODetect.R. image

image

I use Liftover tools to transform the genome build of reference from hg19 to hg38, coding the id as chr:pos:a1:a2, and remove duplicate id from the plink file and ldscore file.

After this, I run the script use:

Rscript ../software/X_Wing/LOGODetect.R --sumstats ./test_CAD_EAS,./test_CAD_EUR --n_gwas 184305,178726 --ref_dir /software/reference/LOGODetect_1kg_ref --pop EUR,EAS --block_partition /LD_reference/ldblock_hg38 --gc_snp /LD_reference/snpid_hg38 --out_dir . --n_cores 8 --target_pop EUR --n_topregion 1000

If you need further information, I'd like to provide my reference file and GWAS file to you.

Thanks a lot in advance if you could help me to solve this.

Best!

ghm17 commented 1 year ago

I think a more convenient way is to transform the genome build of input GWAS summary statistics from hg38 to hg19, which will be less likely to cause inconsitency running the tool. If the error still occurs, maybe you can share the input GWAS files with us to take a deeper look into what's going on.