hsaXXXXX

hsa00100

hsa00120

hsa00130

hsa00140

hsa00190

hsa02010


Each file "hsaXXXXX" contains the gene indetifiers of the pathway


datasets

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.

Claudia Cabrera

genomicper

Circular Genomic Permutation using Gwas p-Values of Association

hsaXXXXX function

Format

Pathways:

Source


KEGG pathways examples


hsaXXXXX: KEGG pathways examples

Description

Usage

Arguments

Format

Pathways:

Source

Examples