Bioconductor-mirror/garfield: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Version 1.5.0

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).

Getting started

Package details

AuthorSandro Morganella <[email protected]>
Bioconductor views Annotation FunctionalPrediction GenomeAnnotation Software StatisticalMethod
MaintainerValentina Iotchkova <[email protected]>
LicenseGPL-3
Version1.5.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("Bioconductor-mirror/garfield")
Bioconductor-mirror/garfield documentation built on June 1, 2017, 9:37 a.m.