genomicper: Circular Genomic Permutation using Gwas p-Values of Association

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.

Version: 1.6
Depends: R (≥ 2.10)
Imports: stats, grDevices, utils, graphics, DBI
Suggests: KEGG.db, reactome.db, AnnotationDbi
Published: 2016-07-05
Author: Claudia P. Cabrera, Pau Navarro, Chris S.Haley
Maintainer: Claudia Cabrera <c.cabrera at qmul.ac.uk>
License: GPL-2
NeedsCompilation: no
CRAN checks: genomicper results

Downloads:

Reference manual: genomicper.pdf
Package source: genomicper_1.6.tar.gz
Windows binaries: r-devel: genomicper_1.6.zip, r-release: genomicper_1.6.zip, r-oldrel: genomicper_1.6.zip
OS X El Capitan binaries: r-release: genomicper_1.6.tgz
OS X Mavericks binaries: r-oldrel: genomicper_1.6.tgz
Old sources: genomicper archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=genomicper to link to this page.