R: Combine results of multiple permutation procedures

combineAnalyses {NetRep} | R Documentation

## Combine results of multiple permutation procedures

### Description

This function takes the output from multiple runs of `modulePreservation`, combines their results, and returns a new set of permutation test P-values. This is useful for parallelising calculations across multiple machines.

### Usage

    combineAnalyses(pres1, pres2)

### Arguments

`pres1, pres2` | lists returned by `modulePreservation`.

### Details

The calls to 'modulePreservation' must have been identical for both input lists, with the exception of the number of threads used and the number of permutations calculated.

### Value

A nested list containing the same elements as `modulePreservation`.

### 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)

    pres1 <- modulePreservation(
     network=network_list, data=data_list, correlation=correlation_list,
     moduleAssignments=labels_list, nPerm=1000, discovery="discovery",
     test="test", nThreads=2
    )

    pres2 <- modulePreservation(
     network=network_list, data=data_list, correlation=correlation_list,
     moduleAssignments=labels_list, nPerm=1000, discovery="discovery",
     test="test", nThreads=2
    )

    combined <- combineAnalyses(pres1, pres2)

[Package NetRep version 1.2.4 Index]