mixSQP

Estimate mixture proportions of a mixture model using
mix-SQP algorithm.

The R package 'ashr' implements an Empirical Bayes
approach for large-scale hypothesis testing and false discovery
rate (FDR) estimation based on the methods proposed in
M. Stephens, 2016, "False discovery rates: a new deal",
<DOI:10.1093/biostatistics/kxw041>. These methods can be applied
whenever two sets of summary statistics---estimated effects and
standard errors---are available, just as 'qvalue' can be applied
to previously computed p-values. Two main interfaces are
provided: ash(), which is more user-friendly; and ash.workhorse(),
which has more options and is geared toward advanced users. The
ash() and ash.workhorse() also provides a flexible modeling
interface that can accommodate a variety of likelihoods (e.g.,
normal, Poisson) and mixture priors (e.g., uniform, normal).

Peter Carbonetto

ashr

Methods for Adaptive Shrinkage, using Empirical Bayes

Matthew Stephens

Chaoxing Dai

David Gerard

Mengyin Lu

Lei Sun

Jason Willwerscheid

Nan Xiao

Mazon Zeng

mixSQP function

<dl><dt>matrix_lik</dt>
<dd>A matrix containing the conditional likelihood
values, possibly normalized.</dd>
<dt>prior</dt>
<dd>A vector of the parameters of the Dirichlet prior on
the mixture weights.</dd>
<dt>pi_init</dt>
<dd>The initial estimate of the mixture weights.</dd>
<dt>control</dt>
<dd>A list of settings for the mix-SQP optimization
algorithm; see <code>mixsqp</code> for details.</dd>
<dt>weights</dt>
<dd>The weights to be assigned to the observations. Must
be a vector of length equal the number of rows of <code>matrix_lik</code>.
If <code>weights = NULL</code>, all observations are assigned the same
weight.</dd></dl>

Arguments

Estimate mixture proportions of a mixture model using
mix-SQP algorithm. — mixSQP

<dl>

<dt>matrix_lik</dt>
<dd>A matrix containing the conditional likelihood
values, possibly normalized.</dd>


<dt>prior</dt>
<dd>A vector of the parameters of the Dirichlet prior on
the mixture weights.</dd>


<dt>pi_init</dt>
<dd>The initial estimate of the mixture weights.</dd>


<dt>control</dt>
<dd>A list of settings for the mix-SQP optimization
algorithm; see <code>mixsqp</code> for details.</dd>


<dt>weights</dt>
<dd>The weights to be assigned to the observations. Must
be a vector of length equal the number of rows of <code>matrix_lik</code>.
If <code>weights = NULL</code>, all observations are assigned the same
weight.</dd>

</dl>

Estimate mixture proportions of a mixture model using
mix-SQP algorithm.

mixSQP: Estimate mixture proportions of a mixture model using mix-SQP algorithm.

Description

Usage

Value

Arguments