R: How many permutations do I need to test at my desired...

requiredPerms {NetRep} | R Documentation

## How many permutations do I need to test at my desired significance level?

### Description

How many permutations do I need to test at my desired significance level?

### Usage

    requiredPerms(alpha, alternative = "greater")

### Arguments

`alpha` | desired significance threshold.
`alternative` | a character string specifying the alternative hypothesis, must be one of "greater" (default), "less", or "two.sided". You can specify just the initial letter.

### Value

The minimum number of permutations required to detect any significant associations at the provided `alpha`. The minimum p-value will always be smaller than `alpha`.

### Examples

    data("NetRep")

    # Set up input lists for each input matrix type across datasets. The list
    # elements can have any names, so long as they are consistent between the
    # inputs.
    network_list <- list(discovery=discovery_network, test=test_network)
    data_list <- list(discovery=discovery_data, test=test_data)
    correlation_list <- list(discovery=discovery_correlation, test=test_correlation)
    labels_list <- list(discovery=module_labels)

    # How many permutations are required to Bonferroni adjust for the 4 modules
    # in the example data?
    nPerm <- requiredPerms(0.05/4)

    # Note that we recommend running at least 10,000 permutations to make sure
    # that the null distributions are representative.

    preservation <- modulePreservation(
     network=network_list, data=data_list, correlation=correlation_list,
     moduleAssignments=labels_list, nPerm=nPerm, discovery="discovery",
     test="test"
    )

[Package NetRep version 1.2.4 Index]