modPres_WGCNA {BioNERO}R Documentation

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

Description

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

Usage

modPres_WGCNA(explist, ref_net, plot_all_stats = FALSE, nPerm = 200)

Arguments

explist

List of expression data frames or SummarizedExperiment objects.

ref_net

Reference network object returned by the function exp2net.

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.

Value

A ggplot object with module preservation statistics.

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 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)


[Package BioNERO version 1.2.0 Index]