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: 2026-07-07 06:53:30 UTC; root
Author: Claudia P Cabrera [aut, cre], Pau Navarro [aut], Chris S Haley
        [aut]
Depends: R (>= 3.5.0)
Repository: https://cran.r-universe.dev
Date/Publication: 2026-02-23 16:10:17 UTC
RemoteUrl: https://github.com/cran/genomicper
RemoteRef: HEAD
RemoteSha: a870ab42a3741aea2457c60bc58ad5cf748fe9df