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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.
| Version: | 1.7 |
| Depends: | R (≥ 3.5.0) |
| Imports: | stats, grDevices, utils, graphics, DBI, reactome.db, AnnotationDbi |
| Published: | 2021-05-08 |
| DOI: | 10.32614/CRAN.package.genomicper |
| Author: | Claudia P Cabrera [aut, cre], Pau Navarro [aut], Chris S Haley [aut] |
| Maintainer: | Claudia P Cabrera <c.cabrera at qmul.ac.uk> |
| License: | GPL-2 |
| NeedsCompilation: | no |
| CRAN checks: | genomicper results |
| Reference manual: | genomicper.pdf |
| Package source: | genomicper_1.7.tar.gz |
| Windows binaries: | r-devel: genomicper_1.7.zip, r-release: genomicper_1.7.zip, r-oldrel: genomicper_1.7.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): genomicper_1.7.tgz, r-oldrel (x86_64): not available |
| Old sources: | genomicper archive |
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