Description Usage Arguments Details Value References
Estimate p-value by comparing a score to its permutations.
1 2 |
eval.v |
A vector of values where the cumulative distribution function should be evaluated. |
score.mat |
A matrix-like object with scores from original data and possibly permutations with rows corresponding to features and columns to simulations. |
alternative |
A character string specifying the alternative hypothesis. |
It's checked that rownames(score.mat)==names(eval.v)
. If a p-value is 1, it results in a z-score of
-Inf, which can produce an error in downstream analysis, so we calculate a new p-value as 1 - 10^(-6).
A matrix with two columns containing z-scores (larger is more significant) & p-values with
nrow = length(eval.v)
.
Phipson B, Smyth GK. Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat Appl Genet Mol Biol. 2010;9:Article39. doi: 10.2202/1544-6115.1585.
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