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

Source: R/network_comparison.R
modPres_netrep.Rd

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

# \donttest{
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")
#> Error in eval(expr, envir, enclos): object 'explist' not found
exp_ortho <- lapply(exp_ortho, function(x) filter_by_variance(x, n=1500))
#> Error in eval(expr, envir, enclos): object 'exp_ortho' not found
# Previously calculated SFT powers
powers <- c(13, 15)
gcn_osa <- exp2gcn(exp_ortho$osa, net_type = "signed hybrid",
                   SFTpower = powers[1], cor_method = "pearson")
#> Error in eval(expr, envir, enclos): object 'exp_ortho' not found
gcn_zma <- exp2gcn(exp_ortho$zma, net_type = "signed hybrid",
                   SFTpower = powers[2], cor_method = "pearson")
#> Error in eval(expr, envir, enclos): object 'exp_ortho' not found
explist <- exp_ortho
#> Error in eval(expr, envir, enclos): object 'exp_ortho' not found
ref_net <- gcn_osa
#> Error in eval(expr, envir, enclos): object 'gcn_osa' not found
test_net <- gcn_zma
#> Error in eval(expr, envir, enclos): object 'gcn_zma' not found
# 10 permutations for demonstration purposes
pres_netrep <- modPres_netrep(explist, ref_net, test_net,
                              nPerm=10, nThreads = 2)
#> Error in eval(expr, envir, enclos): object 'explist' not found
# }