plotFDR: Plot False Discovery Rate (FDR) estimates from output by...

In mixtools: Tools for Analyzing Finite Mixture Models

Plot False Discovery Rate (FDR) estimates from output by EM-like strategies

Description

Plot FDR(p_i) estimates against index of sorted p-values from, e.g., normalmixEM or the semiparametric mixture model posterior probabilities output by spEMsymlocN01, or any EM-algorithm like normalmixEM which returns posterior probabilities. The function can simultaneously plot FDR estimates from two strategies for comparison. Plot of the true FDR can be added if complete data are available (typically in simulation studies).

Usage

plotFDR(post1, post2 = NULL, lg1 = "FDR 1", lg2 = NULL, title = NULL, 
        compH0 = 1, alpha = 0.1, complete.data = NULL, pctfdr = 0.3)

Arguments

post1	The matrix of posterior probabilities from objects such as the output from spEMsymlocN01. The rows need to be sorted by increasing pvalues.
post2	A second object like post1 if comparison is desired, also sorted by increasing pvalues.
lg1	Text describing the FDR estimate in post1.
lg2	Text describing the FDR estimate in post2 if provided.
title	Plot title, a default is provided if NULL.
compH0	The component indicator associated to the null hypothesis H0, normally 1 since it is defined in this way in spEMsymlocN01, but in case of label switching in other algorithms it can be set to 2.
alpha	The target FDR level; the index at which the FDR estimate crosses the horizontal line for level alpha gives the maximum number of cases to reject.
complete.data	An array with n lines and 2 columns, with the component indicator in column 1 and the p-values in column 2, sorted by p-values.
pctfdr	The level up to which the FDR is plotted, i.e. the scale of the vertical axis.

Value

A plot of one or two FDR estimates, with the true FDR if available

Author(s)

Didier Chauveau

References

• Chauveau, D., Saby, N., Orton, T. G., Lemercier B., Walter, C. and Arrouys, D. Large-scale simultaneous hypothesis testing in monitoring carbon content from French soil database – A semi-parametric mixture approach, Geoderma 219-220 (2014), 117-124.

See Also

spEMsymlocN01

mixtools documentation built on Dec. 5, 2022, 5:23 p.m.