Package: genomicper
Type: Package
Title: Circular Genomic Permutation using Genome Wide Association
        p-Values
Version: 1.7
Date: 2021-05-06
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"))
Author: Claudia P Cabrera [aut, cre],
  Pau Navarro [aut],
  Chris S Haley [aut]
Maintainer: Claudia P Cabrera <c.cabrera@qmul.ac.uk>
Imports: stats,grDevices,utils,graphics,DBI,reactome.db,AnnotationDbi
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(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.
License: GPL-2
NeedsCompilation: no
Packaged: 2021-05-06 16:06:27 UTC; PallisDell
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2021-05-08 08:00:05 UTC
Built: R 4.5.2; ; 2025-11-08 02:38:24 UTC; windows
