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Perform module stability analysis

Source: R/gcn_inference.R
module_stability.Rd

Perform module stability analysis

Usage

module_stability(exp, net, nRuns = 20)

Arguments

exp

A gene expression data frame with genes in row names and samples in column names or a `SummarizedExperiment` object.

net

List object returned by exp2gcn.

nRuns

Number of times to resample. Default is 20.

Value

A base plot with the module stability results.

See also

sampledBlockwiseModules

Examples

data(filt.se)
filt <- filt.se[1:100, ] # reducing even further for testing purposes
# The SFT fit was previously calculated and the optimal power was 16
gcn <- exp2gcn(filt, SFTpower = 16, cor_method = "pearson")
#> ..connectivity..
#> ..matrix multiplication (system BLAS)..
#> ..normalization..
#> ..done.
# For simplicity, only 2 runs
module_stability(exp = filt, net = gcn, nRuns = 2)
#>  ...working on run 1 ..
#>  ...working on run 2 ..
#>  ...working on run 3 ..