infer_ancestry

Uses ~20k SNPs selected for common frequency across 5 major super populations

Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper
to make generic calls to the API, plus convenience functions for
specific queries.

Gibran Hemani

ieugwasr

Interface to the 'OpenGWAS' Database API

Ben Elsworth

Tom Palmer

Rita Rasteiro

infer_ancestry function

<dl><dt>d</dt>
<dd>Data frame containing at least <code>rsid</code> and <code>eaf</code> columns.
e.g. output from associations</dd>
<dt>snpinfo</dt>
<dd>Output from <code>afl2_list</code>, <code>afl2_rsid</code> or <code>afl2_chrpos</code>.
If <code>NULL</code> then <code>afl2_list()</code> is used by default</dd>
<dt>opengwas_jwt</dt>
<dd>Used to authenticate protected endpoints. Login to <a href="https://api.opengwas.io">https://api.opengwas.io</a> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.</dd></dl>

Arguments

Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies — infer_ancestry

<dl>

<dt>d</dt>
<dd>Data frame containing at least <code>rsid</code> and <code>eaf</code> columns.
e.g. output from associations</dd>


<dt>snpinfo</dt>
<dd>Output from <code>afl2_list</code>, <code>afl2_rsid</code> or <code>afl2_chrpos</code>.
If <code>NULL</code> then <code>afl2_list()</code> is used by default</dd>


<dt>opengwas_jwt</dt>
<dd>Used to authenticate protected endpoints. Login to <a href='https://api.opengwas.io'>https://api.opengwas.io</a> to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.</dd>

</dl>

infer_ancestry: Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies

Description

Usage

Value

Arguments