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eQTL-Catalogue / eQTL-Catalogue-resources

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Gene level threshold #42

Open Vibha-Acharya opened 1 month ago

Vibha-Acharya commented 1 month ago

Dear eQTLCatalogue team,

We are using eQTL catalogue to discover eQTLs in our selected variants. I have several confusions regarding the datasets and was wondering if you could provide some insights into it.

What is the difference between the .cc.tsv files versus the .all.tsv.gz files in the repository,

Also, we were thinking to apply gene-based threshold similar to GTEx pipeline , where the genome-wide threshold is determined using FDR and beta parameters of the minimum P value from permutation is used to determine the nominal P value threshold for each gene.

Although the p_beta, p_perm are available in *.permutation files, the beta parameters (shape_1, shape_2 aka alpha, beta) are not available.

I wonder if there is a way we can determine the pvalue threshold for each gene for all variants,

Thank you so much,

Regards, Vibha

VitorAguiar commented 1 month ago

I'm not related to the eQTL Catalogue, but regarding your first question, once @kauralasoo told me that the "*.all.tsv.gz" files contain full summary statistics, and "*.cc.tsv.gz" contain all genes that had FDR < 0.01 and at least one fine mapped credible set.