Description Usage Arguments Value
First, estimate empirical p-values based on a comparison of the actual and permuted test statistics. Next, estimate the proportion of true null hypotheses using the qvalue package as well as qvalues from the empirical p-values, using this value. If the estimated pi0 <= 0, then sequentially recalculates using increasingly conservative set of lambda values, until lambda = 0.5.
1 2 | permQValue(dcObject, permObject, secondMat, testSlot, verbose = FALSE,
plotFdr = FALSE, empOnly = FALSE)
|
dcObject |
The original S4 class object containing the test statistics to be extracted. |
permObject |
The array of matrices containing the null test statistics. |
secondMat |
Logical, indicating whether a second matrix was used in the construction of this dcObject and permObject. If FALSE, the upper.tri of both are extracted to avoid double counting test statistics. |
testSlot |
The slot of the dcObject to be removed for use as the actual test statistic. |
verbose |
Whether summaries of the q-value operations should be reported. |
plotFdr |
Allows for plotting of fdrtool p-value adjustment result OR empirical FDR q-value adjustment technique, if either of these are chosen. Requires fdrtool package OR qvalue package. Default = FALSE. |
empOnly |
Whether or not we don't want to calculate qvalues for the empirical pvalues. Default = FALSE. |
A list containing a vectof of empirical p-values and a vector of q-values, both of the same length as the original actual test statistics.
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