calculateEnrichment: Calculate the enrichment of GWAS traits among eQTLs

Description Usage Arguments Value Author(s)

View source: R/annot_gwas.R

Description

Based on Supplementary Figure S16 in (Kumasaka et al 2015).

Usage

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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)

Arguments

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.

Value

list(enrichment = traits enriched among eQTLs, overlap = table of overlapping genes and traits).

Author(s)

Kaur Alasoo


kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.