modPres_netrep {BioNERO} | R Documentation

## Calculate module preservation between two expression data sets using NetRep's algorithm

### Description

Calculate module preservation between two expression data sets using NetRep's algorithm

### Usage

    modPres_netrep(
      explist,
      ref_net = NULL,
      test_net = NULL,
      nPerm = 1000,
      nThreads = 1
    )

### Arguments

`explist` | List of expression data frames or SummarizedExperiment objects.
`ref_net` | Reference network object returned by the function `exp2net`.
`test_net` | Test network object returned by the function `exp2net`.
`nPerm` | Number of permutations. Default: 1000
`nThreads` | Number of threads to be used for parallel computing. Default: 1

### Value

Output list from `NetRep::modulePreservation` and a message in user's standard output stating which modules are preserved.

### See Also

`modulePreservation`

### Examples

    set.seed(1)
    data(og.zma.osa)
    data(zma.se)
    data(osa.se)
    og <- og.zma.osa
    exp_ortho <- exp_genes2orthogroups(explist, og, summarize = "mean")
    exp_ortho <- lapply(exp_ortho, function(x) filter_by_variance(x, n=1500))
    # Previously calculated SFT powers
    powers <- c(13, 15)
    gcn_osa <- exp2gcn(exp_ortho$osa, net_type = "signed hybrid",
                       SFTpower = powers[1], cor_method = "pearson")
    gcn_zma <- exp2gcn(exp_ortho$zma, net_type = "signed hybrid",
                       SFTpower = powers[2], cor_method = "pearson")
    explist <- exp_ortho
    ref_net <- gcn_osa
    test_net <- gcn_zma
    # 10 permutations for demonstration purposes
    pres_netrep <- modPres_netrep(explist, ref_net, test_net,
                                  nPerm=10, nThreads = 2)

[Package BioNERO version 1.0.4 Index]