modPres_netrep: Calculate module preservation between two expression data...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.