SNPsAnnotation


SNPs annotated to genes. Annotation only when the SNPs fall within start and end of transcription of the genes.


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

SNPsAnnotation function

Sample data frame with 339096 SNP observations on the following 6 variables.
  <dl>
    <dt><code>name</code></dt><dd>a character vector</dd> <dt><code>Chromosome</code></dt><dd>a character vector</dd> <dt><code>Location</code></dt><dd>a numeric vector of the SNP location</dd> <dt><code>GENE_ID</code></dt><dd>a numeric vector with entrez geneID</dd> <dt><code>Symbol</code></dt><dd>a character vector ; other annotation slot 1</dd> <dt><code>Orientation</code></dt><dd>a character vector; other annotation slot 2</dd> </dl> <pre>
	name      Chromosome  Location  GENE_ID    Symbol     Orientation
	rs1000313          1  15405489    23254    KIAA1026             +
	rs1000533          1 168282491     9095    TBX19                +
	rs1000731          1 231963491    27185    DISC1                +
	</pre>

Format

NCBI Gene database,(http://www.ncbi.nlm.nih.gov/gene ; Build.37.1).

SNPsAnnotation: SNPs-Genes annotation to Distance 0 (SNPs within a gene)

Description

Usage

Arguments

Format

Source

Examples