Package: genomicper
Type: Package
Title: Circular Genomic Permutation using Genome Wide Association
        p-Values
Version: 1.8
Date: 2026-02-21
Authors@R: c(person(given = c("Claudia", "P"),
                      family = "Cabrera",
                      role = c("aut", "cre"),
                      email = "c.cabrera@qmul.ac.uk"),
               person(given = "Pau",
                      family = "Navarro",
                      role = "aut"),
               person(given = c("Chris", "S"),
                      family = "Haley",
                      role = "aut"))
Maintainer: Claudia P Cabrera <c.cabrera@qmul.ac.uk>
Imports: stats,grDevices,utils,graphics
Description: 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. 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. Cabrera et al (2012) <doi:10.1534/g3.112.002618> .
License: GPL-2
NeedsCompilation: no
Packaged: 2026-02-23 13:56:25 UTC; PallisDell
Author: Claudia P Cabrera [aut, cre],
  Pau Navarro [aut],
  Chris S Haley [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2026-02-23 16:10:17 UTC
Built: R 4.6.0; ; 2026-04-25 11:12:30 UTC; unix
