est_cond

Internal helper function for est_all_cond

Performs the colocalisation tests described in
Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>,
Wallace (2020) <doi:10.1371/journal.pgen.1008720>,
Wallace (2021) <doi:10.1371/journal.pgen.1009440>.

Chris Wallace

coloc

Colocalisation Tests of Two Genetic Traits

Claudia Giambartolomei

Vincent Plagnol

est_cond function

<dl><dt>x</dt>
<dd>coloc dataset</dd>
<dt>LD</dt>
<dd>named matrix of r</dd>
<dt>YY</dt>
<dd>sum((Y-Ybar)^2)</dd>
<dt>sigsnps</dt>
<dd>names of snps to jointly condition on</dd>
<dt>xtx</dt>
<dd>optional, matrix X'X where X is the genotype matrix. If
not available, will be estimated from LD, MAF, beta and sample
size (the last three should be part of the coloc dataset)</dd></dl>

Arguments

Author

generate conditional summary stats — est_cond

<dl>

<dt>x</dt>
<dd>coloc dataset</dd>


<dt>LD</dt>
<dd>named matrix of r</dd>


<dt>YY</dt>
<dd>sum((Y-Ybar)^2)</dd>


<dt>sigsnps</dt>
<dd>names of snps to jointly condition on</dd>


<dt>xtx</dt>
<dd>optional, matrix X'X where X is the genotype matrix. If
not available, will be estimated from LD, MAF, beta and sample
size (the last three should be part of the coloc dataset)</dd>

</dl>

est_cond: generate conditional summary stats

Description

Usage

Value

Arguments

Author