garfield
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Bioconductor version: Release (3.17)
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>
citation("garfield")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| garfield Guide | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Annotation, FunctionalPrediction, GenomeAnnotation, Software, StatisticalMethod |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (7.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | |
| Linking To | |
| Suggests | knitr |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | garfield_1.28.0.tar.gz |
| Windows Binary | garfield_1.28.0.zip |
| macOS Binary (x86_64) | garfield_1.28.0.tgz |
| macOS Binary (arm64) | garfield_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/garfield |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/garfield |
| Bioc Package Browser | https://code.bioconductor.org/browse/garfield/ |
| Package Short Url | https://bioconductor.org/packages/garfield/ |
| Package Downloads Report | Download Stats |