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xqwen / torus

QTL Discovery using Annotations
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Issues with the output results after running enrichment analysis #16

Open netwchao opened 2 months ago

netwchao commented 2 months ago

Thank you for developing the TORUS algorithm. I am trying to investigate the enrichment of H3K27ac signals in liver tissue within its eQTL data. The screenshot below shows the commands I used for performing enrichment analysis with TORUS, along with the output results.

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My output results differ from those in your documentation, despite ensuring that all input data formats match the requirements specified in the documentation (https://github.com/xqwen/torus/tree/master/examples/GTEx_liver). I aimed to investigate the enrichment of H3K27ac peaks in liver eQTL data, but the current output appears to evaluate enrichment across different TSS ranges in liver eQTL data. Could you help me understand the reason behind this discrepancy?

The screenshot below shows the format of the SNP annotation file I used as input.

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@xqwen

LifanLiang commented 1 month ago

I have the same problem. Then I realized the SNP column in the annotation file should align with the SNP id in summary statistics. Once I got them matched. The annotation showed up in the enrichment results.