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daiqile96 / OTTERS

A powerful TWAS framework leveraging summary-level reference data
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Imputing Expression Error: Single SNP models #7

Closed m-mews closed 10 months ago

m-mews commented 11 months ago

I noticed when I was imputing the genetically regulated expression of my genes that I get an error saying "There is no estimated eQTL weights for [method]". However, when I went back to my model weight file, there is a single SNP for that gene. Could you look into this issue? Thank you in advance!

num=0 TargetID=ENSG00000211970 There is no estimated eQTL weights for lsum Done.

cat lsum.txt CHROM POS A1 A2 TargetID ES 14 106645480 C T ENSG00000211970 -0.0499000000000002

daiqile96 commented 11 months ago

What's your input for the --models= parameter? The eQTL weights files are required to have the same names as the models. For example, for --models=lassosum, the eQTL weights file should be named as lassosum.txt.

m-mews commented 10 months ago

I had adjusted the modeling parameter to --models=['P0.001', 'P0.05', 'lsum', 'SDPR', 'PRScs']. Here's another example where each method has a single SNP and I receive the following output. Thank you in advance for looking into this issue!!!

num=0 TargetID=ENSG00000166321 There is no estimated eQTL weights for P0.001 There is no estimated eQTL weights for P0.05 There is no estimated eQTL weights for lsum There is no estimated eQTL weights for SDPR There is no estimated eQTL weights for PRScs Done.

cat lsum.txt CHROM POS A1 A2 TargetID ES 10 73229583 G T ENSG00000166321 -0.7499

cat P0.001.txt CHROM POS A1 A2 TargetID ES 10 73229583 G T ENSG00000166321 -0.22962028

cat P0.05.txt CHROM POS A1 A2 TargetID ES 10 73229583 G T ENSG00000166321 -0.22962028

cat PRScs.txt CHROM POS A1 A2 TargetID ES 10 73229583 G T ENSG00000166321 -0.11472381529486128

cat SDPR.txt CHROM POS A1 A2 TargetID ES 10 73229583 G T ENSG00000166321 -0.229743

daiqile96 commented 10 months ago

Thanks for the example! I used the tabix tool to extract the eQTL weights for each gene, and the first line was skipped, causing this error. I've fixed the bug and updated the OTTERS tool. Could you please try again and let me know if it works for you?

m-mews commented 10 months ago

Thank you so much!!! I re-ran the code and it works this time!