Package: genomicper
Type: Package
Title: Circular Genomic Permutation using Gwas p-Values of Association
Version: 1.6
Date: 2016-07-05
Author: Claudia P. Cabrera, Pau Navarro, Chris S.Haley
Maintainer: Claudia Cabrera <c.cabrera@qmul.ac.uk>
Imports: stats,grDevices,utils,graphics,DBI,
Suggests: KEGG.db,reactome.db,AnnotationDbi
Description: Circular genomic permutation approach uses GWAS results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure. All 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. The SNPs annotation and pathways annotations can be performed within the package or provided by the user.
License: GPL-2
NeedsCompilation: no
Packaged: 2016-07-05 21:14:03 UTC; claudiacc
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2016-07-05 23:42:23
