garfield-package: GARFIELD - GWAS Analysis of Regulatory or Functional...

Description Details Author(s) References See Also


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
Type: Package
Version: 1.0
Date: 2015-12-14
License: GPL-3

See for example analysis usage and garfield.plot for plotting examples.


Sandro Morganella <email:>

Maintainer: Valentina Iotchkova <email:>


Valentina Iotchkova, Graham Ritchie, Matthias Geihs, Sandro Morganella, Josine Min, Klaudia Walter, Nicholas Timpson, UK10K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. In preparation

See Also, garfield.plot

garfield documentation built on Nov. 8, 2020, 11:08 p.m.