genomicper: Circular Genomic Permutation using Genome Wide Association p-Values

Circular genomic permutation approach uses genome wide association studies (GWAS) results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure(Cabrera et al (2012) <doi:10.1534/g3.112.002618>). All single nucleotide polymorphisms (SNPs) in the GWAS are placed in a 'circular genome' according to their location. Then the complete set of SNP association p-values are permuted by rotation with respect to the SNPs' genomic locations. Two testing frameworks are available: permutations at the gene level, and permutations at the SNP level. The permutation at the gene level uses Fisher's combination test to calculate a single gene p-value, followed by the hypergeometric test. The SNP count methodology maps each SNP to pathways/gene-sets and calculates the proportion of SNPs for the real and the permutated datasets above a pre-defined threshold. Genomicper requires a matrix of GWAS association p-values and SNPs annotation to genes. Pathways can be obtained from within the package or can be provided by the user.

Version: 1.7
Depends: R (≥ 3.5.0)
Imports: stats, grDevices, utils, graphics, DBI, reactome.db, AnnotationDbi
Published: 2021-05-08
Author: Claudia P Cabrera [aut, cre], Pau Navarro [aut], Chris S Haley [aut]
Maintainer: Claudia P Cabrera <c.cabrera at qmul.ac.uk>
License: GPL-2
NeedsCompilation: no
CRAN checks: genomicper results

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Reference manual: genomicper.pdf
Package source: genomicper_1.7.tar.gz
Windows binaries: r-devel: genomicper_1.7.zip, r-release: genomicper_1.7.zip, r-oldrel: genomicper_1.7.zip
macOS binaries: r-release: genomicper_1.6.tgz, r-oldrel: not available
Old sources: genomicper archive

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