Description Usage Arguments Details Value Examples
WARNING: Matlab has to be installed on your computer.
1 | markov_stability(dataset, sel, distan, nn, matlab)
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dataset |
Name of the dataset. Either "quake", "sandberg", "bernstein" or "linnarsson" |
sel |
Selection method used by gene_filter2() function (either "none", "correlation", "variance", "variance_weight", "shannon_weight") |
distan |
Distance metrics for calculating a distance matrix (either "pearson", "spearman", "euclidean", "manhattan" or "minkowski"). |
nn |
Number of nearest neighbours used |
matlab |
Path to matlab source file (e.g. "/Applications/MATLAB_R2015a.app/bin/matlab") |
Diffusion times are defined in the interval [10^1:10^5].
File dataset-sel-distan-nn-N.csv containing number of clusters at different diffusion times. File script.m contains a sequence of commands used in Matlab to run Markov stability algorithm.
1 | markov_stability("quake", "none", "spearman", 3, "/Applications/MATLAB_R2015a.app/bin/matlab")
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