exGWAS

An example file of GWAS summary statistics

datasets

The goal of 'snpsettest' is to provide simple tools that perform
set-based association tests (e.g., gene-based association tests)
using GWAS (genome-wide association study) summary statistics. A
set-based association test in this package is based on the
statistical model described in VEGAS (versatile gene-based
association study), which combines the effects of a set of SNPs
accounting for linkage disequilibrium between markers. This package
uses a different approach from the original VEGAS implementation to
compute set-level p values more efficiently, as described in
<https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.

Jaehyun Joo

snpsettest

A Set-Based Association Test using GWAS Summary Statistics

Blanca Himes

exGWAS function

Data frame with columns<dl class="dl-horizontal">
<dt>id</dt><dd>SNP ID.</dd>
<dt>chr</dt><dd>chromosome.</dd>
<dt>pos</dt><dd>base-pair position.</dd>
<dt>A1, A2</dt><dd>allele codes.</dd>
<dt>pvalue</dt><dd>p value.</dd>
</dl>

Format

An example file of GWAS summary statistics — exGWAS

Data frame with columns<dl class='dl-horizontal'>
<dt>id</dt><dd>SNP ID.</dd>
<dt>chr</dt><dd>chromosome.</dd>
<dt>pos</dt><dd>base-pair position.</dd>
<dt>A1, A2</dt><dd>allele codes.</dd>
<dt>pvalue</dt><dd>p value.</dd>
</dl>

exGWAS: An example file of GWAS summary statistics

Description

Usage

Arguments

Format

Examples