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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("garfield")
AuthorSandro Morganella <sm22@sanger.ac.uk>
Bioconductor views Annotation FunctionalPrediction GenomeAnnotation Software StatisticalMethod
Date of publicationNone
MaintainerValentina Iotchkova <vi1@sanger.ac.uk>
LicenseGPL-3
Version1.4.0

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.