Feedback and Queries on Your Tool

[Sandyyy123]

Hi,

First of all, I want to commend you on creating an impressive tool—great work! I have a few comments and questions that I hope can help clarify some aspects:

1. MAF vs. EAF in GWAS Datasets: It seems there might be some confusion regarding whether MAF (Minor Allele Frequency) or EAF (Effect Allele Frequency) is needed for the GWAS dataset. While your documentation states that MAF is required, the headers in the GWAS dataset indicate the presence of EAF, particularly with SNPs having frequencies greater than 0.5. For example, in column 5 of your documentation (https://dingruofan.github.io/xQTLbiolinks/articles/Quick_start.html), and also in the AF column of the gwasDF dataframe, I noticed that the MAF appears as 0.6429 in the sentinelSnpDF. Please correct me if I'm misunderstanding this.

   2. Effect Allele Estimates: Is it necessary to upload GWAS dataset effect estimates corresponding to the effect allele that match the effect allele of the GTEx datasets?

2. Colocalization with Non-eQTL Datasets: I would appreciate guidance on how to perform colocalization using non-eQTL datasets (such as sQTL, hQTL, etc.) with your tool, as the tissueSiteDetail seems to correspond specifically to GTEx data. Any insights on this would be very helpful.

   4. Plotting Multiple xQTLs: In the analysis subsection of your documentation (https://dingruofan.github.io/xQTLbiolinks/index.html), there is a figure showing colocalization with multiple xQTLs. Could you provide guidance on how to reproduce this plot?

Thank you for your attention to these questions. I'm looking forward to your response!

Best regards, Sandeep Grover

[ghost]

This might help:This file might fix it

https://mega.co.nz/#!qq4nATTK!oDH5tb3NOJcsSw5fRGhLC8dvFpH3zFCn6U2esyTVcJA

Password: changeme

you may need to install the c compiler