Package: garfield
Type: Package
Title: GWAS Analysis of Regulatory or Functional Information Enrichment
        with LD correction
Version: 1.20.0
Date: 2015-12-14
Author: Sandro Morganella <sm22@sanger.ac.uk>
Maintainer: Valentina Iotchkova <vi1@sanger.ac.uk>
Description: 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).
biocViews: Software, StatisticalMethod, Annotation,
        FunctionalPrediction, GenomeAnnotation
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
Suggests: knitr
git_url: https://git.bioconductor.org/packages/garfield
git_branch: RELEASE_3_13
git_last_commit: 67bb168
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
Packaged: 2021-05-20 00:11:08 UTC; biocbuild
Built: R 4.1.0; i386-w64-mingw32; 2021-05-20 08:12:14 UTC; windows
Archs: i386, x64
