SummaryConsistency

Data simulated using real genotypes from 10,000
 individuals and 200 SNPs. One SNP have non-zero effect
 on the multivariate response. The response data are generated under
 a linear regression model. There is also one SNP with flipped allele
 between summary statistics and the reference panel.

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

SummaryConsistency function

<code>SummaryConsistency</code> is a list with the following
elements:
<dl> <dt>z</dt>
<dd>z-scores computed by fitting univariate simple regression
 variable-by-variable.</dd>
 <dt>ldref</dt>
<dd>LD matrix estimated from the reference panel.</dd>
 <dt>flip_id</dt>
<dd>The index of the SNP with the flipped allele.</dd>
 <dt>signal_id</dt>
<dd>The index of the SNP with the non-zero effect.</dd></dl>

Format

Simulated Fine-mapping Data with LD matrix From Reference Panel. — SummaryConsistency

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

 <dt>z</dt>
<dd>z-scores computed by fitting univariate simple regression
 variable-by-variable.</dd>


 <dt>ldref</dt>
<dd>LD matrix estimated from the reference panel.</dd>


 <dt>flip_id</dt>
<dd>The index of the SNP with the flipped allele.</dd>


 <dt>signal_id</dt>
<dd>The index of the SNP with the non-zero effect.</dd>

</dl>

SummaryConsistency: Simulated Fine-mapping Data with LD matrix From Reference Panel.

Description

Arguments

Format

See Also

Examples