NetRep (version 1.2.7)

requiredPerms: 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")

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.

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.

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"
)