garfield-package {garfield} | R Documentation

## GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

### Description

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.

### Details

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.

### Author(s)

Sandro Morganella <email: sm22@sanger.ac.uk>

Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>

### References

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.run`, `garfield.plot`

[Package garfield version 1.20.0 Index]