FinemappingConvergence

Data simulated using real genotypes from 50,000
 individuals and 200 SNPs. Two of the SNPs have non-zero effects
 on the multivariate response. The response data are generated under
 a linear regression model. The simulated response and the columns
 of the genotype matrix are centered.

data

Implements methods for variable selection in linear
regression based on the "Sum of Single Effects" (SuSiE) model, as
described in Wang et al (2020) <DOI:10.1101/501114> and Zou et al
(2021) <DOI:10.1101/2021.11.03.467167>. These methods provide
simple summaries, called "Credible Sets", for accurately
quantifying uncertainty in which variables should be selected.
The methods are motivated by genetic fine-mapping applications,
and are particularly well-suited to settings where variables are
highly correlated and detectable effects are sparse. The fitting
algorithm, a Bayesian analogue of stepwise selection methods
called "Iterative Bayesian Stepwise Selection" (IBSS), is simple
and fast, allowing the SuSiE model be fit to large data sets
(thousands of samples and hundreds of thousands of variables).

Peter Carbonetto

susieR

Sum of Single Effects Linear Regression

Gao Wang

Yuxin Zou

Kaiqian Zhang

Matthew Stephens

FinemappingConvergence function

<code>FinemappingConvergence</code> is a list with the following
elements:
<dl> <dt>XtX</dt>
<dd>Summary statistics computed using the centered and
 scaled genotype matrix.</dd>
 <dt>Xty</dt>
<dd>Summary statistics computed using the centered and
 scaled genotype data, and the centered simulated response.</dd>
 <dt>yty</dt>
<dd>yty is computed using the centered simulated response.</dd>
 <dt>n</dt>
<dd>The sample size (50,000).</dd>
 <dt>true_coef</dt>
<dd>The coefficients used to simulate the responses.</dd>
 <dt>z</dt>
<dd>z-scores from a simple (single-SNP) linear regression.</dd></dl>

Format

Simulated Fine-mapping Data with Convergence Problem. — FinemappingConvergence

<code>FinemappingConvergence</code> is a list with the following
elements:
<dl>

 <dt>XtX</dt>
<dd>Summary statistics computed using the centered and
 scaled genotype matrix.</dd>


 <dt>Xty</dt>
<dd>Summary statistics computed using the centered and
 scaled genotype data, and the centered simulated response.</dd>


 <dt>yty</dt>
<dd>yty is computed using the centered simulated response.</dd>


 <dt>n</dt>
<dd>The sample size (50,000).</dd>


 <dt>true_coef</dt>
<dd>The coefficients used to simulate the responses.</dd>


 <dt>z</dt>
<dd>z-scores from a simple (single-SNP) linear regression.</dd>

</dl>

FinemappingConvergence: Simulated Fine-mapping Data with Convergence Problem.

Description

Arguments

Format

See Also

Examples