Package: garfield 1.35.0
Valentina Iotchkova
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).
Authors:
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garfield.pdf |garfield.html✨
garfield/json (API)
NEWS
| # Install 'garfield' in R: |
| install.packages('garfield', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:garfield-1.33.0(bioc 3.20)garfield-1.32.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarestatisticalmethodannotationfunctionalpredictiongenomeannotation
Last updated 23 days agofrom:ff651220ae. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 30 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 30 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 30 2024 |
Exports:garfield_permgarfield_prepgarfield.plotgarfield.plot.fnxgarfield.run
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction | garfield-package garfield |
| Garfield plotting function | garfield.plot |
| Internal radial plotting function for the garfield.plot function | garfield.plot.fnx |
| GARFIELD enrichment analysis function | garfield.run garfield_perm garfield_prep |