markov_stability: Find structure of the data (number of clusters) based on...

Description Usage Arguments Details Value Examples

Description

WARNING: Matlab has to be installed on your computer.

Usage

1
markov_stability(dataset, sel, distan, nn, matlab)

Arguments

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")

Details

Diffusion times are defined in the interval [10^1:10^5].

Value

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.

Examples

1
markov_stability("quake", "none", "spearman", 3, "/Applications/MATLAB_R2015a.app/bin/matlab")

wikiselev/clustools documentation built on May 4, 2019, 5:25 a.m.