GWAS Analysis of Regulatory or Functional Information Enrichment
with LD correction
Description
GARFIELD is a non-parametric functional enrichment
analysis approach described in the paper GARFIELD: GWAS
analysis of regulatory or functional information enrichment
with LD correction. Briefly, it is a method that leverages GWAS
findings with regulatory or functional annotations (primarily
from ENCODE and Roadmap epigenomics data) to find features
relevant to a phenotype of interest. It performs greedy pruning
of GWAS SNPs (LD r2 > 0.1) and then annotates them based on
functional information overlap. Next, it quantifies Fold
Enrichment (FE) at various GWAS significance cutoffs and
assesses them by permutation testing, while matching for minor
allele frequency, distance to nearest transcription start site
and number of LD proxies (r2 > 0.8).