gene.curated.GRCh38

Human gene information was extracted from the GENCODE release 37. This data
only contains 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.GRCh38 function

Data frame with columns<dl>
<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 GRCh38 version — gene.curated.GRCh38

Data frame with columns<dl>
<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.GRCh38: Human gene information from the GENCODE GRCh38 version

Description

Usage

Arguments

Format

Examples