gene.curated.GRCh37

Human gene information was extracted from the GENCODE release 19. This data
only contains 'KNOWN' status genes with the following gene biotypes:
protein-coding, Immunoglobulin (Ig) variable chain and T-cell receptor (TcR)
genes.

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

gene.curated.GRCh37 function

Data frame with columns<dl class="dl-horizontal">
<dt>gene.id</dt><dd>SNP ID.</dd>
<dt>chr</dt><dd>chromosome.</dd>
<dt>start</dt><dd>genomic start location (1-based).</dd>
<dt>end</dt><dd>genomic end location.</dd>
<dt>strand</dt><dd>genomic strand.</dd>
<dt>gene.name</dt><dd>gene symbols mapped to the GENCODE genes.</dd>
<dt>gene.type</dt><dd>gene biotypes in the GENCODE genes.</dd>
</dl>

Format

Human gene information from the GENCODE GRCh37 version — gene.curated.GRCh37

Data frame with columns<dl class='dl-horizontal'>
<dt>gene.id</dt><dd>SNP ID.</dd>
<dt>chr</dt><dd>chromosome.</dd>
<dt>start</dt><dd>genomic start location (1-based).</dd>
<dt>end</dt><dd>genomic end location.</dd>
<dt>strand</dt><dd>genomic strand.</dd>
<dt>gene.name</dt><dd>gene symbols mapped to the GENCODE genes.</dd>
<dt>gene.type</dt><dd>gene biotypes in the GENCODE genes.</dd>
</dl>

gene.curated.GRCh37: Human gene information from the GENCODE GRCh37 version

Description

Usage

Arguments

Format

Examples