garfield-package {garfield} | R Documentation |
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 garfield.run for example analysis usage and garfield.plot for plotting examples.
Sandro Morganella <email: sm22@sanger.ac.uk>
Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>
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
garfield.run
, garfield.plot