module_preservation {BioNERO}

R Documentation

Calculate network preservation between two expression data sets

Description

Calculate network preservation between two expression data sets

Usage

module_preservation(
  explist,
  ref_net = NULL,
  test_net = NULL,
  algorithm = "netrep",
  nPerm = 1000,
  nThreads = 1,
  plot_all_stats = FALSE
)

Arguments

explist	List of SummarizedExperiment objects or expression data frames with genes (or orthogroups) in row names and samples in column names.
ref_net	Reference network object returned by the function exp2gcn.
test_net	Test network object returned by the function exp2gcn.
algorithm	Module preservation algorithm to be used. One of 'netrep' (default, permutation-based) or WGCNA.
nPerm	Number of permutations. Default: 1000
nThreads	Number of threads to be used for parallel computing. Default: 1
plot_all_stats	Logical indicating whether to save all density and connectivity statistics in a PDF file or not. Default: FALSE.

Value

A list containing the preservation statistics (netrep) or a ggplot object with preservation statistics. See WGCNA::modulePreservation or NetRep::modulePreservation for more info.

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 <- module_preservation(explist, ref_net, test_net, nPerm=10)

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