plot_diagnostic

Generate several plots to diagnose the fitness of ASH on the data

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

plot_diagnostic function

<dl><dt>x</dt>
<dd>the fitted ash object</dd>
<dt>plot.it</dt>
<dd>logical. whether to plot the diagnostic result</dd>
<dt>sebetahat.tol</dt>
<dd>tolerance to test the equality of betahat</dd>
<dt>plot.hist</dt>
<dd>logical. whether to plot the histogram of betahat when sebetahat is not constant</dd>
<dt>xmin, xmax</dt>
<dd>range of the histogram of betahat to be plotted</dd>
<dt>breaks</dt>
<dd>histograms parameter (see <code><a href="/link/hist?package=ashr&version=2.2-63" data-mini-rdoc="ashr::hist">hist</a></code>)</dd>
<dt>alpha</dt>
<dd>error level for the de-trended diagnostic plot</dd>
<dt>pch, cex</dt>
<dd>plot parameters for dots</dd></dl>

Arguments

Diagnostic plots for ash object — plot_diagnostic

<dl>

<dt>x</dt>
<dd>the fitted ash object</dd>


<dt>plot.it</dt>
<dd>logical. whether to plot the diagnostic result</dd>


<dt>sebetahat.tol</dt>
<dd>tolerance to test the equality of betahat</dd>


<dt>plot.hist</dt>
<dd>logical. whether to plot the histogram of betahat when sebetahat is not constant</dd>


<dt>xmin, xmax</dt>
<dd>range of the histogram of betahat to be plotted</dd>


<dt>breaks</dt>
<dd>histograms parameter (see <code><a href='https://rdrr.io/r/graphics/hist.html'>hist</a></code>)</dd>


<dt>alpha</dt>
<dd>error level for the de-trended diagnostic plot</dd>


<dt>pch, cex</dt>
<dd>plot parameters for dots</dd>

</dl>

Diagnostic plots for ash object

plot_diagnostic: Diagnostic plots for ash object

Description

Usage

Arguments

Details