modPres_netrep {BioNERO} | R Documentation |
Calculate module preservation between two expression data sets using NetRep's algorithm
modPres_netrep( explist, ref_net = NULL, test_net = NULL, nPerm = 1000, nThreads = 1 )
explist |
List of expression data frames or SummarizedExperiment objects. |
ref_net |
Reference network object returned by the function |
test_net |
Test network object returned by the function |
nPerm |
Number of permutations. Default: 1000 |
nThreads |
Number of threads to be used for parallel computing. Default: 1 |
Output list from NetRep::modulePreservation
and a message in
user's standard output stating which modules are preserved.
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)