Skip to contents

Exact permutation p-values

Source: R/perm_pe.R
permPvals.Rd

Calculates exact p-values for permutation tests when permutations are randomly drawn with replacement. This implementation is based on (slightly adapted) the implementation by Belinda Phipson and Gordon Smyth from the R package statmod

Usage

permPvals(nPermSupObs, nPermEff, totalPossibleNPerm)

Arguments

nPermSupObs

number of permutations that yielded test statistics at least as extreme as the observed data. Can be a vector or an array of values.

nPermEff

number of permutations effectively computed.

totalPossibleNPerm

total number of permutations possible.

Value

a vector (or an array, similar to nperm_supobs) of exact p-values

References

Phipson B, and Smyth GK (2010). Permutation p-values should never be zero: calculating exact p-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology, Volume 9, Issue 1, Article 39. http://www.statsci.org/smyth/pubs/PermPValuesPreprint.pdf

See also

statmod::permp

Author

Belinda Phipson and Gordon Smyth (adapted by Boris Hejblum)

Examples

permPvals(10, 100, 1000)
#> [1] 0.1084109