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

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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, nPerm = 200)

Arguments

explist	List of expression data frames or SummarizedExperiment objects.
ref_net	Reference network object returned by the function exp2net.
nPerm	Number of permutations for the module preservation statistics. It must be greater than 1. Default: 200.

Value

A ggplot object with module preservation statistics.

Examples

set.seed(1)
data(og.zma.osa)
data(zma.se)
data(osa.se)
explist <- list(Zma = zma.se, Osa = 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)

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