CAGE and txrevise promoter usage QTL summary statistics

<p>This dataset contains promoter usage QTL summary statistics obtained using <a href="https://github.com/eQTL-Catalogue/qtlmap">QTLmap</a>. QTLmap_summary_CAGE.txt contains summary statistics for CAGE, QTLmap_summary_txrevise-25.txt for regular <a href="https://github.com/kauralasoo/txrevise">txrevise</a> and QTLmap_summary_txrevise-supplemented-20.txt for txrevise with the new generated annotations.</p> <p>This dataset contains the promoter annotations obtained with CAGE as part of the FANTOM5 project, cleaned and reformatted&nbsp;using <a href="https://github.com/andreasvija/cage/blob/master/qtlmap_prep/clean_promoters.R">this code</a> for the purpose of QTL mapping, that were used to obtain the aforementioned summary statistics. They can be found in Cleaned_FANTOM5_promoter_annotations.tsv.</p> <p>&nbsp;</p> <p>QTL summary statistics column descriptions:</p> <p>molecular_trait_object_id - gene</p> <p>molecular_trait_id - top promoter for the gene</p> <p>n_traits - how many promoters were tested for the gene</p> <p>n_variants - how many genetic variants were tested for the promoter</p> <p>variant - top genetic variant for the promoter</p> <p>chromosome - chromosome</p> <p>position - promoter&#39;s top genetic variant start position</p> <p>pvalue - nominal p-value of the association between the promoter and genetic variant</p> <p>beta - the fitted linear model&#39;s regression coefficent</p> <p>p_perm - empirical p-value calculated using permutations</p> <p>p_beta - estimated empirical p-value based on the beta distribution, this is the recommended p-value column</p>