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 1.0.4 Index]