garfield-package: GARFIELD - GWAS Analysis of Regulatory or Functional...
In garfield: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Description
Details
Author(s)
References
See Also
Description
GARFIELD leverages GWAS findings with regulatory or functional annotations
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 signficance cut-offs 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). Finally, it includes visualization
tools.
Details
Package: garfield
Type: Package
Version: 1.0
Date: 2015-12-14
License: GPL-3
See garfield.run for example analysis usage and garfield.plot for plotting
examples.
Author(s)
Sandro Morganella <email: sm22@sanger.ac.uk>
Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>
References
Valentina Iotchkova, Graham Ritchie, Matthias Geihs, Sandro Morganella,
Josine Min, Klaudia Walter, Nicholas Timpson, UK10K Consortium, Ian Dunham,
Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or
Functional Information Enrichment with LD correction. In preparation
See Also
garfield documentation built on Nov. 8, 2020, 11:08 p.m.
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Description Details Author(s) References See Also
Description
GARFIELD leverages GWAS findings with regulatory or functional annotations 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 signficance cut-offs 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). Finally, it includes visualization tools.
Details
| Package: | garfield |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2015-12-14 |
| License: | GPL-3 |
See garfield.run for example analysis usage and garfield.plot for plotting examples.
Author(s)
Sandro Morganella <email: sm22@sanger.ac.uk>
Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>
References
Valentina Iotchkova, Graham Ritchie, Matthias Geihs, Sandro Morganella, Josine Min, Klaudia Walter, Nicholas Timpson, UK10K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. In preparation
See Also
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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