phenoscanner

The <code>phenoscanner</code> function queries the PhenoScanner database of genotype-phenotype associations from inside R.

Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.

Stephen Burgess

MendelianRandomization

Mendelian Randomization Package

Olena Yavorska

James Staley

Fernando Hartwig

Jim Broadbent

Christopher Foley

Andrew Grant

Amy Mason

Ting Ye

Haoran Xue

Zhaotong Lin

Siqi Xu

Ashish Patel

Hyunseung Kang

Sheng Wang

Ville Karhunen

phenoscanner function

<dl><dt>snpquery</dt>
<dd>a vector of SNPs.</dd>
<dt>genequery</dt>
<dd>a vector of gene names.</dd>
<dt>regionquery</dt>
<dd>a vector of genomic regions.</dd>
<dt>catalogue</dt>
<dd>the catalogue to be searched (options: None, GWAS, eQTL, pQTl, mQTL, methQTL).</dd>
<dt>pvalue</dt>
<dd>the p-value threshold.</dd>
<dt>proxies</dt>
<dd>the proxies database to be searched (options: None, AFR, AMR, EAS, EUR, SAS).</dd>
<dt>r2</dt>
<dd>the r2 threshold.</dd>
<dt>build</dt>
<dd>the genome build (options: 37, 38).</dd></dl>

Arguments

PhenoScanner &lt;phenoscanner@gmail.com&gt;

Author

PhenoScanner — phenoscanner

<dl>

<dt>snpquery</dt>
<dd>a vector of SNPs.</dd>


<dt>genequery</dt>
<dd>a vector of gene names.</dd>


<dt>regionquery</dt>
<dd>a vector of genomic regions.</dd>


<dt>catalogue</dt>
<dd>the catalogue to be searched (options: None, GWAS, eQTL, pQTl, mQTL, methQTL).</dd>


<dt>pvalue</dt>
<dd>the p-value threshold.</dd>


<dt>proxies</dt>
<dd>the proxies database to be searched (options: None, AFR, AMR, EAS, EUR, SAS).</dd>


<dt>r2</dt>
<dd>the r2 threshold.</dd>


<dt>build</dt>
<dd>the genome build (options: 37, 38).</dd>

</dl>

PhenoScanner

phenoscanner: PhenoScanner

Description

Usage

Value

Arguments

Author

Examples