garfield: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

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@sanger.ac.uk>
Date of publication
None
Maintainer
Valentina Iotchkova <vi1@sanger.ac.uk>
License
GPL-3
Version
1.2.0

View on Bioconductor

Man pages

garfield-package
GARFIELD - GWAS Analysis of Regulatory or Functional...
garfield.plot
Garfield plotting function
garfield.plot.fnx
Internal radial plotting function for the garfield.plot...
garfield.run
GARFIELD enrichment analysis function

Files in this package

garfield/DESCRIPTION
garfield/NAMESPACE
garfield/R
garfield/R/garfield.plot.R
garfield/R/garfield.run.R
garfield/build
garfield/build/vignette.rds
garfield/inst
garfield/inst/NEWS.Rd
garfield/inst/doc
garfield/inst/doc/vignette.Rnw
garfield/inst/doc/vignette.pdf
garfield/inst/extdata
garfield/inst/extdata/annotation
garfield/inst/extdata/annotation/chr22
garfield/inst/extdata/annotation/link_file.txt
garfield/inst/extdata/maftssd
garfield/inst/extdata/maftssd/chr22
garfield/inst/extdata/pval
garfield/inst/extdata/pval/trait
garfield/inst/extdata/pval/trait/chr22
garfield/inst/extdata/tags
garfield/inst/extdata/tags/r01
garfield/inst/extdata/tags/r01/chr22
garfield/inst/extdata/tags/r08
garfield/inst/extdata/tags/r08/chr22
garfield/man
garfield/man/garfield-package.Rd
garfield/man/garfield.plot.Rd
garfield/man/garfield.plot.fnx.Rd
garfield/man/garfield.run.Rd
garfield/src
garfield/src/garfield_init.c
garfield/src/garfield_perm.cpp
garfield/src/garfield_prep.cpp
garfield/vignettes
garfield/vignettes/vignette.Rnw