ld_reflookup

Provide a list of rsids that you may want to perform LD operations on to
check if they are present in the LD reference panel. If they are not then
some functions e.g. <code>ld_clump</code> will exclude them from the analysis,
so you may want to consider how to handle those variants in your data.

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

ld_reflookup function

<dl><dt>rsid</dt>
<dd>Array of rsids to check</dd>
<dt>pop</dt>
<dd>Super-population to use as reference panel. Default = <code>"EUR"</code>.
Options are <code>"EUR"</code>, <code>"SAS"</code>, <code>"EAS"</code>, <code>"AFR"</code>, <code>"AMR"</code></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.#' @param bfile If this is provided then will use the API. Default = <code>NULL</code></dd></dl>

Arguments

Check which rsids are present in a remote LD reference panel — ld_reflookup

<dl>

<dt>rsid</dt>
<dd>Array of rsids to check</dd>


<dt>pop</dt>
<dd>Super-population to use as reference panel. Default = <code>"EUR"</code>.
Options are <code>"EUR"</code>, <code>"SAS"</code>, <code>"EAS"</code>, <code>"AFR"</code>, <code>"AMR"</code></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.#' @param bfile If this is provided then will use the API. Default = <code>NULL</code></dd>

</dl>

ld_reflookup: Check which rsids are present in a remote LD reference panel

Description

Usage

Value

Arguments