demo


GWAS p-values (tab delimited file). 
First Column must contain the SNP ids and the column name = "name"


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

demo function

A data frame with SNPs identifiers and gwas p-values of association
  <dl>
    <dt><code>name</code></dt><dd>a character vector</dd> <dt><code>abpi</code></dt><dd>a numeric vector</dd> <dt><code>abpilba</code></dt><dd>a numeric vector</dd> <dt><code>abpildfa</code></dt><dd>a numeric vector</dd> <dt><code>abpilpta</code></dt><dd>a numeric vector</dd> <dt><code>abpirba</code></dt><dd>a numeric vector</dd> <dt><code>abpirdfa</code></dt><dd>a numeric vector</dd> <dt><code>abpirpta</code></dt><dd>a numeric vector</dd> <dt><code>alb</code></dt><dd>a numeric vector</dd> <dt><code>avdbp</code></dt><dd>a numeric vector</dd> </dl> <pre>
	name       abpi      abpilba    abpildfa  abpilpta  abpirba   abpirdfa
	rs10000010 0.9122360 0.30088096 0.2332038 0.5193068 0.1255104 0.07253145 
	rs10000023 0.8642906 0.52064064 0.9243443 0.7177759 0.9512171 0.81716250 
	rs10000030 0.2832705 0.99021664 0.8359339 0.9662707 0.8491221 0.50208681 </pre>

demo: GWAS p_values demo data

Description

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Examples