modPres_WGCNA {BioNERO} | R Documentation |
Calculate module preservation between two expression data sets using WGCNA's algorithm
modPres_WGCNA(explist, ref_net, plot_all_stats = FALSE, nPerm = 200)
explist |
List of expression data frames or SummarizedExperiment objects. |
ref_net |
Reference network object returned by the function |
plot_all_stats |
Logical indicating whether to save all density and connectivity statistics in a PDF file or not. Default is FALSE. |
nPerm |
Number of permutations for the module preservation statistics. Default: 200. |
A ggplot object with module preservation statistics.
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 power powers <- c(13, 15) gcn_osa <- exp2gcn(exp_ortho$osa, net_type = "signed hybrid", SFTpower = powers[1], cor_method = "pearson") explist <- exp_ortho ref_net <- gcn_osa # 5 permutations for demonstration purposes pres_wgcna <- modPres_WGCNA(explist, ref_net, nPerm=5)