calculate_local_consistency {transite} | R Documentation

## Local Consistency Score

### Description

C++ implementation of Local Consistency Score algorithm.

### Usage

    calculate_local_consistency(x, numPermutations, minPermutations, e)

### Arguments

`x` | numeric vector that contains values for shuffling
`numPermutations` | maximum number of permutations performed in Monte Carlo test for consistency score
`minPermutations` | minimum number of permutations performed in Monte Carlo test for consistency score
`e` | stop criterion for consistency score Monte Carlo test: aborting permutation process after observing `e` random consistency values with more extreme values than the actual consistency value

### Value

list with `score`, `p_value`, and `n` components, where `score` is the raw local consistency score (usually not used), `p_value` is the associated p-value for that score, obtained by Monte Carlo testing, and `n` is the number of permutations performed in the Monte Carlo test (the higher, the more significant)

### Examples

    poor_enrichment_spectrum <- c(0.1, 0.5, 0.6, 0.4,
      0.7, 0.6, 1.2, 1.1, 1.8, 1.6)
    local_consistency <- calculate_local_consistency(poor_enrichment_spectrum,
      1000000, 1000, 5)

    enrichment_spectrum <- c(0.1, 0.3, 0.6, 0.7, 0.8,
      0.9, 1.2, 1.4, 1.6, 1.4)
    local_consistency <- calculate_local_consistency(enrichment_spectrum,
      1000000, 1000, 5)

[Package transite version 1.8.0 Index]