GPD-Permutation-Test: Implementation of the GPD-based p-value estimation algorithm
In omicsEye/deepath: Generic Omics Pathway Enrichment Analysis

GPD Permutation Test

R Documentation

Implementation of the GPD-based p-value estimation algorithm

Description

Implementation of the GPD-based p-value estimation algorithm

Usage

gpd_permutation_test(
  x0,
  y,
  minM_epdf = 10,
  Nexc = 250,
  Nexc_shrink = 10,
  Nexc_alpha = 0.05,
  yfun,
  ystart = 200,
  ygrow = 100,
  ymax = 5000
)

Arguments

`x0`	an input vector of values
`y`	an input vector of values
`minM_epdf`	a minimumn number of iterations for EPDF
`Nexc`	a number of permution to performe in each step default 250
`Nexc_shrink`	default 10
`Nexc_alpha`	default 0.05
`yfun`	default
`ystart`	default 200
`ygrow`	default 100
`ymax`	default 5000

Value

a 'pvalue'

References

Implementation of the GPD-based p-value estimation algorithm from Knijnenburg, Wessels, Reinders, and Shmulevich (2009) Fewer permutations, more accurate P-values. Bioinformatics 25(12): i161–i168. DOI: 10.1093/bioinformatics/btp211 Implemented by Jason Lloyd-Price and Ali Rahnavard