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.

Author
Claudia P. Cabrera, Pau Navarro, Chris S.Haley
Date of publication
2016-07-05 23:42:23
Maintainer
Claudia Cabrera <c.cabrera@qmul.ac.uk>
License
GPL-2
Version
1.6

View on CRAN

Man pages

demo
GWAS p_values demo data
genes_permutation
Gene-level Permutations
genome_order
Genome Order
genomicper-package
Circular Genomic Permutations
get_pathways
Pathways
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

Files in this package

genomicper
genomicper/NAMESPACE
genomicper/data
genomicper/data/hsa00100.rda
genomicper/data/hsa00120.rda
genomicper/data/demo.rda
genomicper/data/hsa02010.rda
genomicper/data/SNPsAnnotation.rda
genomicper/data/hsa00190.rda
genomicper/data/hsa00140.rda
genomicper/data/hsa00130.rda
genomicper/R
genomicper/R/get_results.R
genomicper/R/read2_paths.R
genomicper/R/genome_order.R
genomicper/R/hyprbg.R
genomicper/R/genes_permutation.R
genomicper/R/plot_results.R
genomicper/R/snps_permutation.R
genomicper/R/get_pathways.R
genomicper/R/read_pvals.R
genomicper/MD5
genomicper/DESCRIPTION
genomicper/man
genomicper/man/genomicper-package.Rd
genomicper/man/demo.Rd
genomicper/man/snps_permutation.Rd
genomicper/man/plot_results.Rd
genomicper/man/read_pvals.Rd
genomicper/man/genes_permutation.Rd
genomicper/man/hsaXXXXX.Rd
genomicper/man/SNPsAnnotation.Rd
genomicper/man/hyprbg.Rd
genomicper/man/genome_order.Rd
genomicper/man/get_results.Rd
genomicper/man/read2_paths.Rd
genomicper/man/get_pathways.Rd