ld_clump_local

Wrapper for clump function using local plink binary and ld reference dataset

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_clump_local function

<dl><dt>dat</dt>
<dd>Dataframe. Must have a variant name column (<code>variant</code>) and pval column called <code>pval</code>.
If <code>id</code> is present then clumping will be done per unique id.</dd>
<dt>clump_kb</dt>
<dd>Clumping kb window. Default is very strict, <code>10000</code></dd>
<dt>clump_r2</dt>
<dd>Clumping r2 threshold. Default is very strict, <code>0.001</code></dd>
<dt>clump_p</dt>
<dd>Clumping sig level for index variants. Default = <code>1</code> (i.e. no threshold)</dd>
<dt>bfile</dt>
<dd>If this is provided then will use the API. Default = <code>NULL</code></dd>
<dt>plink_bin</dt>
<dd>Specify path to plink binary. Default = <code>NULL</code>.
See <a href="https://github.com/explodecomputer/plinkbinr">https://github.com/explodecomputer/plinkbinr</a> for convenient access to plink binaries</dd></dl>

Arguments

Wrapper for clump function using local plink binary and ld reference dataset — ld_clump_local

<dl>

<dt>dat</dt>
<dd>Dataframe. Must have a variant name column (<code>variant</code>) and pval column called <code>pval</code>.
If <code>id</code> is present then clumping will be done per unique id.</dd>


<dt>clump_kb</dt>
<dd>Clumping kb window. Default is very strict, <code>10000</code></dd>


<dt>clump_r2</dt>
<dd>Clumping r2 threshold. Default is very strict, <code>0.001</code></dd>


<dt>clump_p</dt>
<dd>Clumping sig level for index variants. Default = <code>1</code> (i.e. no threshold)</dd>


<dt>bfile</dt>
<dd>If this is provided then will use the API. Default = <code>NULL</code></dd>


<dt>plink_bin</dt>
<dd>Specify path to plink binary. Default = <code>NULL</code>.
See <a href='https://github.com/explodecomputer/plinkbinr'>https://github.com/explodecomputer/plinkbinr</a> for convenient access to plink binaries</dd>

</dl>

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ld_clump_local: Wrapper for clump function using local plink binary and ld reference dataset

Description

Usage

Value

Arguments

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Description

Usage

Value

Arguments

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