Description Usage Arguments Value Author(s)
Based on Supplementary Figure S16 in (Kumasaka et al 2015).
1 2 3 | calculateEnrichment(gwas_catalog, gwas_snp_pvalues, eqtl_lead_snps,
gene_id_name_map, n_genes = 14163, p_diff_thresh = 3,
min_genes_per_trait = 20)
|
gwas_catalog |
EBI GWAS catalog imported using the importGwasCatalog function. |
gwas_snp_pvalues |
FastQTL eQTL pvalues for each SNP in the GWAS catalog, from importGwasPvalue. |
eqtl_lead_snps |
Lead eQTL SNPs for each significant gene. |
gene_id_name_map |
- data frame with two columns: gene_id, gene_name. |
n_genes |
Total numner of genes used in the eQTL analysis. |
p_diff_thresh |
Log10 p-value difference between lead eQTL SNP and lead GWAS SNP. |
min_genes_per_trait |
Minimal number of unique genes per trait to be used for enrichment analysis. |
list(enrichment = traits enriched among eQTLs, overlap = table of overlapping genes and traits).
Kaur Alasoo
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.