garfield-package

garfield

GARFIELD leverages GWAS findings with regulatory or functional annotations
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 signficance cut-offs 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). Finally, it includes visualization
tools.

package

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).

garfield-package: GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Description

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