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).
plotFDR(post1, post2 = NULL, lg1 = "FDR 1", lg2 = NULL, title = NULL,
compH0 = 1, alpha = 0.1, complete.data = NULL, pctfdr = 0.3)A plot of one or two FDR estimates, with the true FDR if available
The matrix of posterior probabilities from objects such as the output
from spEMsymlocN01. The rows need to be sorted by increasing pvalues.
A second object like post1 if comparison is desired, also sorted by increasing pvalues.
Text describing the FDR estimate in post1.
Text describing the FDR estimate in post2 if provided.
Plot title, a default is provided if NULL.
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.
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.
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.
The level up to which the FDR is plotted, i.e. the scale of the vertical axis.
Didier Chauveau
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.
spEMsymlocN01