BIOCONDUCTOR . ORG {
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Title:
Bioconductor - garfield
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).
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Keywords {🔍}
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Topics {✒️}
org/packages/garfield source repository joint galaxy/bioconductor conference bioconductor release tgz source repository source package find features relevant bioconductor support site release //code functional information enrichment quantifies fold enrichment functional information overlap roadmap epigenomics data performs greedy pruning minor allele frequency gz windows binary zip macos binary tgz macos binary package installed pdf reference manual leverages gwas findings gwas significance cutoffs git clone https details biocviews package packages started install gwas analysis functional annotations paper garfield garfield guide bioconductor //bioconductor ld correction pdf news gwas snps ld proxies org registration open permutation testing quietly = true older versions gpl-3 depends developer access download stats released version devel version statisticalmethod version view documentation system requirements
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