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martinjzhang / scDRS

Single-cell disease relevance score (scDRS)
https://martinjzhang.github.io/scDRS/
MIT License
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custom gene set ? #73

Closed zhangpicb closed 10 months ago

zhangpicb commented 10 months ago

Dear @KangchengHou ,

Thanks for your great tool!

I have a question about make custom gene set. I read the custom gene set.

Step2 --snp-loc ${magma_dir}/g1000_eur.bim ,1kg SNPs are used.

But before I read the issue,I use the SNPs in the GWAS summary data to annotate gene,and then using the output file to Step3.

I follow (https://github.com/martinjzhang/scDRS/issues/2) to get gene set. And I find the these 2 output gene.out files are different. Maybe Step2 --snp-loc should use SNPs in GWAS summary?

Thanks in advanced!


# Step 2: make gene annotation file for MAGMA using the following command, this only needs to be done
# once for different GWAS summary statistics, and the file will be saved to out/step1.genes.annot
mkdir -p out/step1
${magma_dir}/magma \
    --annotate window=10,10 \
    --snp-loc ${magma_dir}/g1000_eur.bim \
    --gene-loc ${magma_dir}/NCBI37.3.gene.loc \
    --out out/step1
KangchengHou commented 10 months ago

Yes you can use your .bim file. Just create .bim file that match with your GWAS summary.

zhangpicb commented 10 months ago

Thanks for your quick reply!