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.
|Author||Claudia P. Cabrera, Pau Navarro, Chris S.Haley|
|Date of publication||2016-07-05 23:42:23|
|Maintainer||Claudia Cabrera <firstname.lastname@example.org>|
demo: GWAS p_values demo data
genes_permutation: Gene-level Permutations
genome_order: Genome Order
genomicper-package: Circular Genomic Permutations
get_results: Circular Permutation Results
hsaXXXXX: KEGG pathways examples
hyprbg: Hypergeometric Test (phyper)
plot_results: Plot Results Circular Permutation
read2_paths: Read to SNPs to sets; Map SNPs to gene-sets/pathways
read_pvals: Read GWAS p-values of association and Merge with SNP...
SNPsAnnotation: SNPs-Genes annotation to Distance 0 (SNPs within a gene)
snps_permutation: SNP-level permutations