garfield

DOI: 10.18129/B9.bioc.garfield    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see garfield.

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Bioconductor version: 3.9

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).

Author: Sandro Morganella <sm22 at sanger.ac.uk>

Maintainer: Valentina Iotchkova <vi1 at sanger.ac.uk>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("garfield")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("garfield")

 

PDF		garfield Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, FunctionalPrediction, GenomeAnnotation, Software, StatisticalMethod
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	GPL-3
Depends
Imports
LinkingTo
Suggests	knitr
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Depends On Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	garfield_1.12.0.tar.gz
Windows Binary	garfield_1.12.0.zip
Mac OS X 10.11 (El Capitan)	garfield_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/garfield
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/garfield
Package Short Url	https://bioconductor.org/packages/garfield/
Package Downloads Report	Download Stats